2.1.647 28-04-2012 FAT32 format now starts first cluster at 1MB boundary. NTFS format will start 1st partition at sector 2048 instead of 63. Both these changes lead to >10% speed advantage when copying small files to a USB flash drive.
If FAT32 is selected, then the FAT32 partition will still begin at sector 63 (if no CHS overrides selected), however the number of reserved sectors is chosen so that the first file cluster starts at a 1MB boundary. This seems to improve small file write performance under Windows 7 by at least 10%.
If NTFS is selected (and no other CHS overrides), then the 1st partition will begin at sector 2048. This also seems to lead to better small file write performance under Win 7.
I have not tested performance gains under XP...