Try the following:
 Boot your working system using cpus=1 maxmem=2048......
 Use Disk Utility to format your backup volume as MS-DOS (FAT32) and then re-format it again as Mac OS Extended (Journaled)......
 When you run Carbon Copy Cloner, selecting your working drive as the source and your backup as the target, choosing to clone all files on the source to the target......
 Then re-install Chameleon 2.0 RC5 bootloader on your backup volume.....
Thanks CCC worked before I saw this post but thanks anyway lol I think it was the fact that I was cloning to a partition that wasnt the next physical one on the disc because all the other settings were the same. Will try out those terminal commands and report back.
EDIT: Seems that Chameleon broke my installation somehow, I installed RC5 which gave a "Still waiting for root device" error. I could still boot into it from my Atkos DVD so I installed RC2 like in the main guide and that stalled aswell. It also gave me the USB problem again on my backup partition when I booted from Atkos. Today I'm going to wipe the main partition that has the Chameleon install on it to see if it fixes it. Before that though I'm going to try with those boot files. BTW I installed both while in the Backup partition, I told the installer to install to the Main volume.
EDIT 2: couldn't get the boot file stuff to work so I deleted the main partition. My backup partitions usb problems are now gone. Does this mean that there's some sort of incompatibility with chameleon and my system? I'm going to see if i can install Chimera, the other bootloader.
EDIT 3: That also gave me "waiting for root device". I think its because I dont have an /Extra directory because the Chimera installer mentioned that it needs .com.apple.chameleon.plist in there and not .com.apple.Boot.plist. How can I go about fixing this? I'm really stumped on this one lol
EDIT (again lol) : I was messing about with making an /Extra directory on the Main partition from the Backup partition. Of course it didnt work lol and for some reason it also made the USB problem come back with the Backup partition. Deleted both the Main and Backup partitions, first formatted to FAT and then back to Mac Journaled. I finished cloning Vanilla (still working at the time) to Backup (the next physical volume) and the USB's gone again. Its also gone from Vanilla now. Is this some kext incompatibility?
Im currently trying to reinstall SL on a completely different 40GB drive. This will be my "Vanilla" drive and I made two partitions on the old drive, Backup and Main in that order. This should at least determine if its a problem with the drive somehow.
-----Right, this time as soon as it finished installing on my 40GB drive I copied it to my backup volume from the Retail install disc. Both worked. Then I unplugged the 40GB and booted from the Backup to copy to the Main. During the backup (with disc utility) it froze and now the Backup is unusable because of the USB error. Im booting back into the retail mac disc now to copy the 40GB drive files onto the Backup again.
-----Its working again, but in Safe Mode (-x) the USB doesnt work, and during bootup there are a lot of "AppleUSBEHCI" errors with lots of different letters and numbers after each. These messages come in blocks of 5 or 10 with the occasional other message in between like "DSMOS has arrived". Any ideas on this?
-----Chameleon refuses to install now. It fails at Post Install Actions. Although I did try it and put all the kexts that you said to in E/E and changed the boot file, it is still saying "Still waiting for root device" when I try and boot straight from the HDD without my Atkos DVD.
BTW Cloning from the Install DVD is having a 100% success rate currently lol
EDIT: AHA! I GOT CHAMELEON WORKING! Like a fool I forgot to put com.apple.Boot.plist in /Extra ....
Now I can finally get to work with those terminal commands after I get my graphics sorted. After a backup of course