I had the same problem putney had when i was going DL30. But for me, it was the debugging mode that was getting unchecked for some reason. I went in to titanium, it prompted that i should have debugging on, so i went back out hit debugging, went back in and it prompted me again, went through it again a 3rd time. Prompted me again, so I ignored it, went to restore everything and had the problem putney was having. I ended up just rebooting the phone, made sure i hit debugging, went in and no problem.
P.S. i was not going out of titanium with the home button. I made sure i escaped the program properly but for some reason it was happening.