Dunno about ZIPs, but I always format my card on the MPC first and then transfer stuff to and from my computer.
Just an update on my previous post:
Even after stripping the WAV files, removing all OSX specific files, creating directories on the MPC first, etc., I still can't get cards to work properly between the MPC and OSX. The only real solution that I could find so you don't have to reboot every time you want to move samples (with an Intel mac) is to run XP through a program called Parallels. You can set Parallels to automatically see the card once you connect it to your computer and then you can just transfer files from OSX to your Parallels XP environment and then to the flash/SD card. Hope this helps someone.
Also, if anyone can figure out a way to solve the directory problem with OSX and MPC cards, please let us know

Here is the test:
1. Format the SD/CF card on the MPC.
2. Connect the card to your Mac.
3. Copy over some files and folders (at least 2 levels deep).
4. Load the card into your MPC.
5. Go into the deepest folder you made.
6. Try to use the cursor to get back to the ROOT directory without ejecting or reloading the card (i.e. just using the left cursor button).