What were you using to clone or create those backups?
Apple Disk Utility? SuperDuper? CCC?
Do you own and use Disk Warrior 4.2 to rebuild directories?
One note I wasn't aware of: TimeMachine directory can be too large and DW is not able to work on those drives.
What if you check those drives with Lion Disk Utility and verify the drive/permissions?
I'd even try Recovery Mode and check those drives.
Did you do clone your system before putting Lion on it? erase+install or upgrade?
Make/model of external units? Were they online during use of Lion? indexed by Spotlight or anything?
Not easy but would be interesting to unplug your SSD and try, if that is only internal boot volume and only place you have Lion. Plus, I would invest in another (yes) backup drive just for Lion clone, and / or split a large drive for Lion TimeMachine and clone; and keep everything else separate.
Two OSs for now, two backup sets for each.
CCC and SuperDuper as well as Clone X 4 are probably your best way to clone Mac OS that I know of.