The compress function for Zip (library/Zend/Filter/Compress/Zip.php:108) uses the DIRECTORY_SEPARATOR witch in normal usage is fine but when zip file is created in windows and extracted in linux file patches are messed up.
for example i have a directory structure like this :
dir1/
--file1
--dir2/
----file2
if this directory compressed in windows and extracted in linux i get :
2 directory and 2 files all in the root with names like below

dir1
dir1\file1
dir1\dir2
dir1\dir2\file2

note that dir1\file1 is not a path but the actual file name

the simplest solution would be to use / instead of the DIRECTORY_SEPARATOR or provide on option that the user can set the character for directory separator manually