I just went through and completely reconstructed the pack from my resources, I made sure that i didn't have the minecraft.jar in there, and I'm still getting the parsing error while unzipping the pack. I even used a different compression tool this time.
EDIT: Okay, so i went through, and pushed a version of the pack every time I introduced a mod, and Millenaire is causing the problem. Could it have something to do with the fact that the contents of the "put in mods folder" are not, themselves, zip files?
EDITAGAIN: So, that's what was causing the unzipping errors.
Unfortunately, zipping the folders up (both individually, and as a group) causes the game to not see millenaire for some reason. I guess i'll just have to do without millenaire... q.q