There have been many weird things happening when compiling the source code.
For empty's mod, it was some various crashing bugs that dealt with areas of the code that he didn't modify. For mine, occassionally when I compile the source, it would flicker all the lights in the level. But upon recompiling a few times, the problem would go away. I'm not sure if that would be the case for your problem here, but it's worth a shot.
Also, the newer source is to be released later this month (or at least, a lot of people are hoping so), so I suggest waiting until then to try modifying some source. That way, you won't get TOO into understanding this source, and be fresh and free to understand the newer one with bug fixes and upgrades and all that stuff.
Best of luck.
The one and only,
~PlystirE~
Urlforce:
Dude, I'd rather be declared a dbpro noob than an fpsc legend any day!