Can I sync folders from a fat32 partition with UbuntuOne?

Your partition is likely mounted outside your home folder; Ubuntu One doesn’t support syncing files that aren’t in your home folder, as described at Why not sync folders outside home with Ubuntu One?. That answer also has some discussion of syncing from other partitions and why you should be wary of it, so if you decide to mount your FAT partition in your home folder in order to make it syncable, please read that answer first to discover why that’s potentially not a good idea.