I removed the enhanced graphics pk3 files (xflats, xgfx, xwalls), just to make sure they weren't causing issues. Got past the 2 guards at the start (veteran difficulty), and accepted the first quest (go waste the guy being held prisoner). Dropped into the river, ran into the hidden sewer, and when it would have loaded the next part of the map in the sewer entry, it crashed with a segmentation violation.

Init: Adding ./basev/common/basepak.pk3
Init: adding .\basev\strife/strife1.wad
Init: adding .\basev\strife/voices.wad
Init: Adding ./basev/strife/basepak.pk3
Init: Strife textures detected
Init: Strife textures detected
Init: Winsock TCP/IP Initialised
DevNet: TCP/IP address INADDR_ANY
Parsing
Importing packages
Parsing
Importing packages
Parsing
Importing packages
Defining constants
Defining structs
Defining classes
Defining struct members
Defining class members
Emiting classes
Defining constants
Defining structs
Defining classes
Defining struct members
Defining class members
Emiting classes
Parsing
Importing packages
Defining constants
Defining structs
Defining classes
Defining struct members
Defining class members
Emiting classes
Defining constants
Defining structs
Defining classes
Defining struct members
Defining class members
Emiting classes
Init: Parsing DECORATE definition files
Init: Processing DECORATE scripts
Log: Unsupported flag oldradiusdmg in BossBrain
Log: Unsupported flag fixmapthingpos in KlaxonWarningLight
Init: Post-procesing
Parsing
Importing packages
Defining constants
Defining structs
Defining classes
Defining struct members
Defining class members
Emiting classes
Init: Selected DirectSound sound device
Init: ======================================
Init: Initialising DirectSound driver.
Init: Selected Windows multimedia system midi device
Init: Selected Windows CD audio device
Dev: CDAudio: drive not ready
Init: CDAudio_Init: No CD in player.
Init: CD Audio Initialised
Init: No HW channels available
Init: Using 8 sound buffers
Init: Selected Win32 OpenGL rasteriser device
Init: Parsing effect defs
Init: No such sprite alco
Init: No such sprite alco
Log: Executing startup.vs
Log: Executing default.cfg
Log: Executing config.cfg
Log: Can't find autoexec.cfg
Init: Stencil buffer available
Init: Swap control extension found.
Log: 1600x1200x32.
Init: GL_VENDOR: ATI Technologies Inc.
Init: GL_RENDERER: ATI Radeon HD 4800 Series
Init: GL_VERSION: 3.2.9704 Compatibility Profile Context
Init: GL_EXTENSIONS:
Init: - GL_AMDX_name_gen_delete
Init: - GL_AMDX_vertex_shader_tessellator
Init: - GL_AMD_draw_buffers_blend
Init: - GL_AMD_performance_monitor
Init: - GL_AMD_seamless_cubemap_per_texture
Init: - GL_AMD_shader_stencil_export
Init: - GL_AMD_texture_cube_map_array
Init: - GL_AMD_texture_texture4
Init: - GL_AMD_vertex_shader_tessellator
Init: - GL_ARB_color_buffer_float
Init: - GL_ARB_copy_buffer
Init: - GL_ARB_depth_buffer_float
Init: - GL_ARB_depth_clamp
Init: - GL_ARB_depth_texture
Init: - GL_ARB_draw_buffers
Init: - GL_ARB_draw_buffers_blend
Init: - GL_ARB_draw_elements_base_vertex
Init: - GL_ARB_draw_instanced
Init: - GL_ARB_fragment_coord_conventions
Init: - GL_ARB_fragment_program
Init: - GL_ARB_fragment_program_shadow
Init: - GL_ARB_fragment_shader
Init: - GL_ARB_framebuffer_object
Init: - GL_ARB_framebuffer_sRGB
Init: - GL_ARB_geometry_shader4
Init: - GL_ARB_half_float_pixel
Init: - GL_ARB_half_float_vertex
Init: - GL_ARB_imaging
Init: - GL_ARB_instanced_arrays
Init: - GL_ARB_map_buffer_range
Init: - GL_ARB_multisample
Init: - GL_ARB_multitexture
Init: - GL_ARB_occlusion_query
Init: - GL_ARB_pixel_buffer_object
Init: - GL_ARB_point_parameters
Init: - GL_ARB_point_sprite
Init: - GL_ARB_provoking_vertex
Init: - GL_ARB_seamless_cube_map
Init: - GL_ARB_shader_objects
Init: - GL_ARB_shader_texture_lod
Init: - GL_ARB_shading_language_100
Init: - GL_ARB_shadow
Init: - GL_ARB_shadow_ambient
Init: - GL_ARB_sync
Init: - GL_ARB_texture_border_clamp
Init: - GL_ARB_texture_buffer_object
Init: - GL_ARB_texture_compression
Init: - GL_ARB_texture_compression_rgtc
Init: - GL_ARB_texture_cube_map
Init: - GL_ARB_texture_cube_map_array
Init: - GL_ARB_texture_env_add
Init: - GL_ARB_texture_env_combine
Init: - GL_ARB_texture_env_crossbar
Init: - GL_ARB_texture_env_dot3
Init: - GL_ARB_texture_float
Init: - GL_ARB_texture_mirrored_repeat
Init: - GL_ARB_texture_multisample
Init: - GL_ARB_texture_non_power_of_two
Init: - GL_ARB_texture_query_lod
Init: - GL_ARB_texture_rectangle
Init: - GL_ARB_texture_rg
Init: - GL_ARB_texture_snorm
Init: - GL_ARB_transpose_matrix
Init: - GL_ARB_uniform_buffer_object
Init: - GL_ARB_vertex_array_bgra
Init: - GL_ARB_vertex_array_object
Init: - GL_ARB_vertex_buffer_object
Init: - GL_ARB_vertex_program
Init: - GL_ARB_vertex_shader
Init: - GL_ARB_window_pos
Init: - GL_ATI_draw_buffers
Init: - GL_ATI_envmap_bumpmap
Init: - GL_ATI_fragment_shader
Init: - GL_ATI_meminfo
Init: - GL_ATI_separate_stencil
Init: - GL_ATI_texture_compression_3dc
Init: - GL_ATI_texture_env_combine3
Init: - GL_ATI_texture_float
Init: - GL_ATI_texture_mirror_once
Init: - GL_EXT_abgr
Init: - GL_EXT_bgra
Init: - GL_EXT_bindable_uniform
Init: - GL_EXT_blend_color
Init: - GL_EXT_blend_equation_separate
Init: - GL_EXT_blend_func_separate
Init: - GL_EXT_blend_minmax
Init: - GL_EXT_blend_subtract
Init: - GL_EXT_compiled_vertex_array
Init: - GL_EXT_copy_buffer
Init: - GL_EXT_copy_texture
Init: - GL_EXT_draw_buffers2
Init: - GL_EXT_draw_instanced
Init: - GL_EXT_draw_range_elements
Init: - GL_EXT_fog_coord
Init: - GL_EXT_framebuffer_blit
Init: - GL_EXT_framebuffer_multisample
Init: - GL_EXT_framebuffer_object
Init: - GL_EXT_framebuffer_sRGB
Init: - GL_EXT_geometry_shader4
Init: - GL_EXT_gpu_program_parameters
Init: - GL_EXT_gpu_shader4
Init: - GL_EXT_histogram
Init: - GL_EXT_multi_draw_arrays
Init: - GL_EXT_packed_depth_stencil
Init: - GL_EXT_packed_float
Init: - GL_EXT_packed_pixels
Init: - GL_EXT_pixel_buffer_object
Init: - GL_EXT_point_parameters
Init: - GL_EXT_provoking_vertex
Init: - GL_EXT_rescale_normal
Init: - GL_EXT_secondary_color
Init: - GL_EXT_separate_specular_color
Init: - GL_EXT_shadow_funcs
Init: - GL_EXT_stencil_wrap
Init: - GL_EXT_subtexture
Init: - GL_EXT_texgen_reflection
Init: - GL_EXT_texture3D
Init: - GL_EXT_texture_array
Init: - GL_EXT_texture_buffer_object
Init: - GL_EXT_texture_buffer_object_rgb32
Init: - GL_EXT_texture_compression_latc
Init: - GL_EXT_texture_compression_rgtc
Init: - GL_EXT_texture_compression_s3tc
Init: - GL_EXT_texture_cube_map
Init: - GL_EXT_texture_edge_clamp
Init: - GL_EXT_texture_env_add
Init: - GL_EXT_texture_env_combine
Init: - GL_EXT_texture_env_dot3
Init: - GL_EXT_texture_filter_anisotropic
Init: - GL_EXT_texture_integer
Init: - GL_EXT_texture_lod
Init: - GL_EXT_texture_lod_bias
Init: - GL_EXT_texture_mirror_clamp
Init: - GL_EXT_texture_object
Init: - GL_EXT_texture_rectangle
Init: - GL_EXT_texture_sRGB
Init: - GL_EXT_texture_shared_exponent
Init: - GL_EXT_texture_snorm
Init: - GL_EXT_texture_swizzle
Init: - GL_EXT_timer_query
Init: - GL_EXT_transform_feedback
Init: - GL_EXT_vertex_array
Init: - GL_EXT_vertex_array_bgra
Init: - GL_IBM_texture_mirrored_repeat
Init: - GL_KTX_buffer_region
Init: - GL_NV_blend_square
Init: - GL_NV_conditional_render
Init: - GL_NV_copy_depth_to_color
Init: - GL_NV_explicit_multisample
Init: - GL_NV_primitive_restart
Init: - GL_NV_texgen_reflection
Init: - GL_SGIS_generate_mipmap
Init: - GL_SGIS_texture_edge_clamp
Init: - GL_SGIS_texture_lod
Init: - GL_SUN_multi_draw_arrays
Init: - GL_WIN_swap_hint
Init: - WGL_EXT_swap_control
Init: Maximum texture size: 8192
Init: Found GL_ARB_multitexture...
Init: Multitexture extensions found.
Log: Max texture units: 8
Init: Max anisotropy 16.000000
Init: Clamp to edge extension found.
Init: Found GL_ARB_vertex_shader, GL_ARB_fragment_shader...
Init: Shader extensions found.
Init: Shading language version: 1.50
Init: Max texture image units: 16
Init: Max vertex uniform components: 1024
Init: Max varying floats: 64
Init: Max vertex attribs: 16
Init: Max fragment uniform components: 1024
Init: Found OpenGL 2.0 separate stencil methods
Init: Found GL_ARB_depth_clamp...
Init: Found GL_EXT_stencil_wrap...
Init: Found GL_ARB_vertex_buffer_object...
Init: Vertex buffer object extensions found.
Init: Found GL_EXT_draw_range_elements...
Init: Draw range elements extensions found.
Dev: Spawning server map02
Log: GB: Map goes from (-1088,2176) to (5272,10488)

Log: GB: Creating Segs...

Dev: Server spawned
Log: ---------------------------------------
Log: AREA  2: town
Log: 
Dev: 0 subdivides
Dev: 0 seg subdivides
Dev: 0k light mem
Dev: Client level loaded
Log: You picked up the Medical kit.
Log: You picked up the clip of bullets.
Log: You picked up the clip of bullets.
Log: You picked up the clip of bullets.
Log: You picked up the clip of bullets.
Log: You picked up the clip of bullets.
Log: You picked up the Medical kit.
Log: <-------------------------------->
Log: You don't have the key
Log: <-------------------------------->
Dev: Spawning server map01
Log: GB: Map goes from (656,4472) to (3600,6232)

Log: GB: Creating Segs...

Dev: Server spawned
Log: ---------------------------------------
Log: AREA  1: sanctuary
Log: 
Dev: 0 subdivides
Dev: 0 seg subdivides
Dev: 0k light mem
Dev: Client level loaded
Log: - VMMSystemMidiDevice::Stop
Log: - VAudio::PlaySong
Log: - VAudio::CmdMusic
Log: - COMMAND Music
Log: - VCommand::ExecuteString
Log: - VCmdBuf::Exec
Log: - Host_Frame
Log: Doing C_Shutdown
Log: Doing CL_Shutdown
Log: PLAYER left the game

Log: Doing SV_Shutdown
Log: Doing delete GNet
Log: Doing delete GInput
Log: Doing V_Shutdown
Log: Doing delete GAudio
Log: Doing T_Shutdown
Log: Doing Sys_Shutdown
Log: Doing delete GSoundManager
Log: Doing R_ShutdownTexture
Log: Doing R_ShutdownData
Log: Doing VCommand::Shutdown
Log: Doing VCvar::Shutdown
Log: Doing ShutdownMapInfo
Log: Doing FL_Shutdown
Log: Doing W_Shutdown
Log: Doing GLanguage.FreeData
Log: Doing ShutdownDecorate
Log: Doing VObject::StaticExit
Log: Doing VName::StaticExit
Uninitialised: Doing Z_Shutdown


ERROR: Segmentation Violation

Oddly enough, with those additional graphics files removed, it now takes 11-12 hits with the dagger, to take out a guard. I think there's some memory stomping happening. Was taking 8 hits before, with those graphics files. Edit: I must have been on crack, or I just popped into a parallel reality... Now, regardless of which files I use (and even with zDoom), it takes 11+ hits to take out a guard with the dagger.

The game should also probably not load the same files multiple times.

The crash you are getting is related to MIDI music player, it's not a Vavoom problem, but a Windows mixer problem, you should use Timidity to avoid this crash. Everything else is working as expected.

Groovy, installing Timidity seemed to do the trick.