I have ben importing a user account from another computer. That user account has exactly the same username and password as the old one. At first I could not use it as the permissions where to messed up, and Repair Disk Permissions did not correct them. Then I used Batchmod to change all of them and now I can use it. But I know that some permissions are not right, and Repair Disk Permissions don't change them nor dus it recognize that permissions are wrong. As you say, it looks like they don't need to be repaird. I also tried to change some manually and it's ok.
Also when I start the machine the "?" is first blinking before it finds the operating system? (yes I have the right system/startup disk chosen)