FWIW, both to the OP and those attempting to answer him, I actually did run into such problems when I switched from the ZHLT2.5.3 compile tools I had been using quite successfully to the new (at the time) ZHLT 3.0 tools. A map which had compiled successfully with 2.5.3 now triggered a "Fatal Error" in HLBSP.exe (or possibly HLCSG.exe).
After spending some time tracking down an increasing list of problems - everything I managed to get passed revealed another crash further down the chain - I gave up and went back to 2.5.3 because, hey, it worked.
I recently tried out 3.3 or 3.4 and ran into similar issues. I'm still using 2.5.3.
If such problems were normal, they would undoubtedly have been fixed long ago, so I can only assume there is some particular system configuration which causes the new compile tools to become unstable. However, since 2.5.3 still gets the job done, I really havben't been interested in spending any time trying to figure it out...
shrug
*EDIT*: I suspect my reply probably belongs in the other thread Sidon linked, rather than this one. Sorry...