DO NOT run "rm -rf .*" as a ROOT user!
This will ATTEMPT to remove .. recursively -- which is the parent directory (and if your original folder was /root, that is the filesystem's root folder!)
Instead, try
rm -rf .??*
The ?'s force there to be a character there... so it will remove everything that starts with a dot, then has at least 2 characters after it... the only things that MIGHT be missed would be something named something-like .a
....
Now, on to the actual question... it sounds to me like you're running startx from a command line prompt, and are expecting GNOME or KDE to startup. This is not the general case...
When you startup a GUI, there are actually 2 things that startup:
1) the X-Windows subsystem (effectively, startx), and
2) a Display Manager (GNOME, KDE, or whatever)
If you look in your inittab file, you'll see that you are probably running a script called "prefdm" for runlevel 5. (the full path is "/etc/X11/prefdm" -- and if you look at THAT file, you'll see how it starts up the "default" display manager).
It is perfectly OK to login to a console CLI and run the prefdm script from there.
Good Luck!
Dan
IT4SOHO