Hmmm... thinking you are also using the old DOS PKUNZIP which only handles 8.3 file structure. (not sure, just a guess)

Please make sure you are using the WinZip 9 compliant Command Line tools which support long file names.

Also take a look at this posting which might be of interest or help you further.

Recursive Zip
http://www.kixtart.org/ubbthreads/showflat.php?Cat=&Number=75192