Couple issues need some help with

I had a job related issue at work and it had me and my boss stumped on.

first one is

I logged onto a employee's account with my admin login I ran a windows update, ran a spybot sweep and a synmatic sweep, I then used ccleaner to clear out the temp and clean up some registry with it.

So after I was done with her computer I logged off, when she logged on her windows task bar was half empty and half full the left hand side where the ie and mail icons sit on the top of the taskbar window and the recent programs were empty. So I figured it just cleared the recent programs list. I opened a few programs and they never appeared on the taskbar. I also found I went to IE (yes I know firefox is superior but business wants to use ie7)and it kept rotating between the runonce and microsoft never loading the respective pages but then going back in a continuous loop. I have no idea what happened I tried a system restore rolling it back 3 weeks, then when I realized i made a mistake (panicked when she said she lost her files ) I returned to its normal date. Not sure what happened after that the computer just refuse to do anything in her profile my profile worked fine any ideas?

The second issue I had, after running my cleaning (without ccleaner this time) The guy logged into his account and immideatly got a security message over his login (when it loads personal preferences) he had to click ok twice to get to his desktop. He went to check his mail (outlook express 2003) and for some odd reason it made him go through configuration like it was a fresh copy. As we configured it we got to the info part and we could not perform the test email saying username and password will not work. the server info was att.yahoo.com, he is using a sbcglobal.net email account too. We have no idea why it looked like a fresh copy of outlook when he logged in. We are also wondering if his mail will still be intact from this.

both systems use windows xp
i didn't copy their complete specs so I can't provide them