I formatted my card in "MS-DOS" format using Disk Utility in Mac OSX 10.4.5 and it seems to be working fine for me.
The only reason I had to format it was that it started to behave badly with some files refusing to move or be deleted and some strange error messages when I tried reading or writing to it in the Finder. It was a Sandisk 1Gb card which came pre-formatted, so I blanked it in OSX (zeroing the data) and now it is behaving reliably. (So far)
The only problem you need to watch out for is the Resource Fork Emulation Files which are duplicates of your real files beginning with _, so just make sure you're not trying to load those in some cases where an app lets you see them. There is a little utility for OSX which cleans them away when you eject a disk but I can't recall what it's called at the moment...
Other than that perhaps you could use Virtual PC or something like Disk Warrior? try Versiontracker or Google too and let me know what you find out...
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