Any chance your OS is hiding the .zip extension? When you are re-zipping a file, are you selecting the folders named textures, scripts, vm, etc instead of the folder all those were extracted into (has to end up as z-mod.pk3/textures, not z-mod.pk3/z-mod/textures)? You could also try posting a 'broken' pk3 so we can see what is wrong with it.