Windows has a VERY important system file called the REGISTRY. It contains all the important information to help Windows run successfully.
It seems you get your message when the registry has become corrupt.
Windows does "back up" the registry so it may be that when you rebooted it knew the registry was corrupt and loaded a backup one.
Not sure how "safe" your computer now is so I would make a backup of all your important files in case it happens again and you cannot even get into Windows.
Here is an example of one person who got your problems.
http://www.daniweb.com/forums/thread18179.html
Notice that restarting your PC and pressing F8 will take you into a special Windows start up procedure when you can choose "load last known good configuration".
This will help you if it happens again.