I restarted Fedora Core 6 and then programs don't open in windows, programs don't have a minimise, close, maximize or anything else.. they cannot be moved aswell. The bar at the top of the screen with Applications menu and so on.. is covered by this browser (firefox) I cannot move it because there is nowhere to click. It isn't part of the panel at the bottom of the screen.

Anyone help me.. I went to Administration (or something.. I can't see it right now) and then Windows and it says there is no configuration file for Windows.. as an error.. is there a way I can reinstall whatever makes the windows part work?

First, I would restart it again and see if the behavior is consistent. If it consistenly misbehaves on restart, then re-installing some portion may be more trouble than simply re-installing the whole thing.

I've seen this happen when a startup program is run without the & function so might be worth checking startup scripts. Also you should be able to move windows by holding alt and clicking inside window.

I reinstalled it all and reformatted, but for some reason a lot of times on 5th disk it has a filename error, which was kind of annoying, but I'm ok now.

I found out what the problem was, I tried 2 different ATi drivers today..and both had the same problem. I uninstalled them luckily and it goes back to normal after restart - ati-x11-drv