As for uncompressing from a Perl script, you would probably make your task easier by using a CPAN module instead of forking and execing a shell, something like Archive::Zip or Compress::Bzip2 (and your prerequisite "I can't install modules" is wrong - please read this.)

UPDATE: (today is UPDATE day, by the way)
Found some relevant docs in the gunzip man page:

Files created by zip can be uncompressed by gzip only if they have a single member compressed with the 'deflation' method. This feature is only intended to help conversion of tar.zip files to the tar.gz format. To extract zip files with several members, use unzip instead of gunzip.

UPDATE 2: (told ya)
Disregard everything i have said about bzip2 ... i thought i had used it in the past, but that was something else ... bzip2 only decompresses zip files that have been created with bzip2.

jeffa

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)