Sorry for the double, but this is a bit of a required bump.
Okay, so I can successfully decompile maps. By that, I mean that I run the decompiler and get a .map. I've tried both methods I'd discovered of decompiling. Through command prompt (as described earlier in this thread) and the shortcut > properties > target method (create a shortcut, right click it, navigate to the shortcut tab, and in the target bit, put in "C:\Program Files\Tremulous\netradiant-392-win32\q3map2.exe" -game [game abbreviation] -convert -format map
where [game abbreviation] is trem, in this case. Both result in the same thing. That thing is a .map that is empty of all brushes and entities. I'm entirely unsure of what the issue is, but it's incredibly irritating.