offlineimap uses ":" as suffix separator so, as you mention, you can't make it point to use a FATpartition. There's no configuration option, so we're kind of stuck to non-FAT partitions (which you sure should have). Only patching offlineimap would help, I found this, about running it under Cygwin: http://wiki.yobi.be/wiki/Courier-Cygwin#Offlineimap. I didn't try it though...

Cheers,
Seb