Matt, the message after reboot isn't telling you to put things back, it's merely notifying you that changes have been made.  If you put a checkmark in the box on the lower left of that window, you won't get the message again.  It does indeed sound like you have virus(es) or spyware at the very least.  Do an internet search for a free download of ccleaner.exe which will empty your cookies, and temporary everything files.  You'll also want a good free antivirus program (AVG and Avast are excellent free programs) and a good free antispyware program ("spybot Search and Destroy" and "Ad-Aware SE Personal" are super - make sure you get the free versions only).

 

After you've gotten these programs onto your computer and have it capable of running, reboot into safe mode (power on, gently tap the F8 key after you see the manufacturer's startup screen - you will then see a black screen with white writing - and choose "Safe Mode") You'll always want to run these programs in this mode, because only a minimal number of drivers are loaded - most spyware won't start in safe mode.  As for antivirus,  I like Avast because once it's loaded, it asks if you want it to run at next start up - when you say yes and reboot, it scans for viruses before they are loaded - this might take a long while depending on the size of your hard drive.  Avast will ask you to register your product, but you just need to give them a valid email address and they'll mail you a free registration code.  No further hassles - I've had this running on my machine for almost a year and they've never emailed me or harassed me even once.  Sorry, I sound like a salesman!  But since they're free I guess that doesn't count.

 

I have done this procedure on literally hundreds of computers and it fixes 99 percent of them.  After you are back up and running, make sure you run ccleaner often and defragment your hard drive.

 

Hope this helps.