I use Gentoo Linux and I did plenty of upgrading. The main parts were upgrading the kernel, system and world. Everything seemed to go well except now I can not su from a user account and X will not start at all. I ensured my user accounts were in the correct groups so I can su. I think wheel is the group that allows suing. I added a test user instructed by the Gentoo manual but it was the same results. I must of screwed up some sort of package or permissions got mixed up after this happened. It seems to respond fine in root. I can startx in root just fine. sudo works for users. I suspect I must do something in the /dev directory in order to resolve this. I'm not going to go step by step telling you every detail of what I did and just let you ask me stuff. Im kind of tired.

Permissions issues are always fun!

I can understand being tired (and sick of the sight of a blinking cursor), but you're not going to get much help by telling us you did a bunch of stuff and we need to play 20 questions to find out what you did. If you've done a major upgrade (along with the editing of config files that can go with that) then it could be anything.

You may have already seen this, but if not I recommend reading through http://www.catb.org/~esr/faqs/smart-questions.html after you've had a rest

EDIT: P.S. If it's just messed up permissions, I assume you've tried chown -R username:groupname /home/username?