I've figured out the problem here...For some reason, the Bionic file system is not seeing pre-existing directories on the sd card. Copying to the pc, formatting the card and copying back to the card does not fix it. If you plug the phone into a pc (mine is Win 7), you actually get two hard drives pop up, the internal and the sd card. For a hack/fix, if you copy whatever directories that you need (like Titanium Backup, LPP, ect, to the root of the internal drive, you backups will be seen and work. The long term problem with this is that the internal hard drive, although 16 gig, only has 8 gig available. If you have 10 to 15 gig of stuff on your card that you need the phone to see/use, you've got a problem.
Some one smarter than me needs to figure out how to make the phone see the data on the sd card.