In that case i recommend pk3 edition, which loads automatically. Most probably UIE is launching next map without specific gamedir, which is required for mod to load. This is normal, but not desired in your case. Maybe you could try adding this to launch parameters @ UIE, if it supports it: +set fs_game vogon +set sv_pure 0. If you need sv_pure 1 then use pk3, because Q3 has problems running pure 1 + non-pk3 mods.