Are you placing skill settings for both objects correctly? In doom builder when you see the properties of an object you can see that it has very easy, easy, normal, etc. flags as checkboxes, make sure that all of them are checked, also make sure that single player is checked too, if it isn't it might be why the things you are placing aren't displayed in the game, it has nothing to do with Vavoom's doom builder configuration.
EDIT: Maybe this guide will help you out: [url:2p8fgqob]http://drsleep.newdoom.com/data/doombuilderguide.pdf