I had the same problem when i was trying to update to Ixtreme 1.4(from Ixtreme 1.2) . I was using FWToolbox 4.6. When I tried to do a differential flash restore to restore the drive back to the original fw I got "I can see a lot of differences, make sure you know what you are doing before flash". I used slax 2.0 to put the drive in ModeB and took a few tries (IMG:
style_emoticons/default/uhh.gif) before FWToolbox could do the restore. I used my onboard SATA (intel 945P chipset) and a xecuter connectivity kit NE.
1. Put the drive in to ModeB with Slax 2.0(tried with slax 2.1 (IMG:
style_emoticons/default/grr.gif) and gave up)
2. eject the drive tray at windows startup logo
3. used halo3 and manually closed the tray.,
4. took a few tries(remove the drive from device manager and scan for hardware change) before I could get FWtoolbox to do a restore without complaining about lot of differences.
hope it helps you bro