This does sound quite familiar, although I haven't run into it happening again yet...  Take a test account (one that is having troubles) and delete it from DNN, then test it again. 

DanBall, what happens may sound strange. A year ago we have done bulk import of users from AD to DNN. After that import, any new AD user is created automatically in DNN after it visits the DNN site for the first time.

What we've done now as a part of test is the following:
 
FIRST GROUP OF USERS

- Users who were bulk imported in DNN, but who had NEVER actually logged on to DNN before upgrade - they cannot log on, either automatically or manually. It says something like "Bad username/password".
- When we delete those users from DNN and ask them to log on again on their computers with AD credentials, those users are now automatically logged to our DNN site. They don't have to provide their credentials and they remain logged in DNN site indefinitely.

SECOND GROUP OF USERS

- Users who have been successfully logging on to DNN site before upgrade MUST now enter their credentials to log on to DNN site, but SOME of them cannot login because of invalid username/pass.
- When we deleted those “problematic” users from DNN, they were not created in DNN after logon/logoff in windows and browsing to DNN site, so we must create them manually.
- After creating them manually, they CAN log to DNN site, but, after a custom period of time, they get logged out. The same happens if they close the browser and visit DNN site again - they must enter username/password.

THIRD GROUP OF USERS

- It's just me in this group. Whenever i return to DNN website, I get logged in automatically.

So there are two major problems:

1. Users who have been visiting DNN site in past now must EVERY time enter their credentials, which is VERY annoying to them.
2. Some of them can not log to DNN site at all - deleting and recreating them doesn't help.

Please, advise!
Thanks.