Loading backups crashes and requires firmware reinstall

PS3 Slim 160GB

I've been trying to figure out where I have gone wrong for hours now so I hope someone can help. Now whenever I try to load a backup from Gaia Manager or multiMAN the game will begin to load then seconds later I get a black screen saying "connect the controller using the USB cable". I then have to reinstall the firmware in order to get the PS3 to work. This happens every single time I try to boot a backup.

Here are the steps I have taken so far:

1. Updated 3.40 to 3.41
2. Used E3 dongle to jailbreak 3.41 (backups worked perfectly)
3. Updated to OFW 3.55
4. Updated to Kmeaw CFW 3.55
5. Installed multiMAN 1.13.00 (managed to copy backup from external HDD to internal HDD and boot successfully but always froze during gameplay)
6. Decided to downgrade back to 3.41(3,56) because of freezing using E3 dongle and this guide: PS3 Firmware 3.55 Downgrade Released | PS3 Hacks :: PS3 Homebrew :: PS3 Downloads … -released/
7. Downgraded from 3.41(3,56) to OFW 3.40
8. Updated from OFW 3.40 to OFW 3.41
9. Installed Gaia Manager and multiMAN (This is when the boot problems started)
10. Updated to OFW 3.55
11. Updated to Kmeaw CFW 3.55
12. Installed Gaia Manager and multiMAN (Still the same boot problems)
13. Entered recovery mode and tried everyone restore/rebuild option, deleted every installed .pkg, reinstalled .pkgs (still nothing)

The games on the discs boot perfectly fine but the backups do not, even though they did before. I'm sure I've screwed up somewhere so any help would be greatly appreciated.

Many thanks

Format and reinstall. Start from scratch. Sorry to say, but this is the only way to start over and make sure things are right.