I have a the same problem. i have been using my rooted t1 since january but it got stuck while reading in Repligo. Had to reset it and this time apps lost permissions or how ever you say that. First tried in terminal the fix_permission call but didn't work like before and later i was not allowed to write anything in terminal, by than superuser stoped working too, all apps force closing.
I got adb shell running on my windows pc but when i try to connect to the t1 i get the device not found message.
I don't know if i have shared enough information to get someone to help me, i'm not an android guru
, i just learn while trying out new things.
Thanks in advance.