Did you reboot your phone after you clicked unknown sources? I know it sounds silly, but I had to do that myself. Try again after that. Should work. Also ensure that you really are rooted first, and that you've set superuser permissions to TB.
Other than that, I haven't a clue, as the beauty of TB is that you can completely wipe your phone, install a custom ROM, and still restore your apps. In turn, the same holds true then for when you switch phones. I didn't have to transfer anything from my old sd card, just installed TB to access all my apps from before. TB also offers TB Media Sync to transfer files like your pics and music from one phone to another.
Also, are you using gingerbreak or an actual custom recovery img? Gingerbreak didn't work for me like it should. There are custom recovery img's now. I can't post links but a quick google search should get you there. TJStyle and isaacj87 both have custom recovery img's. I'm using TJstyle's and it works great. isaacj87 is close to a CM7 release also, just waiting on Motorola to release the kernel source code. I'll most likely switch to his CWM when he finishes that build.
Hope that helps.