perhaps OSX does something wierd with the gp2x's libraries....it's usually always hiding a lot of the linux/unix stuff underneath. A whole directory/file structure can just be an icon in the Finder-windows.
perhaps you should go console and copy the files over that way....
I have a mac and a pc, use both with a cardreader to put stuff on the gp2x. Haven't connected the gp2x through USB. Almost never did that with my gp32's either....