Sometimes they get into the registry files and get started up every time the computer starts.

I had a bad one years ago when I was using free virus software, that I had to learn how to go into those files to fully delete the baddie.
It was so long ago I don't recall how to do it again..
After 2 complete system crashes I decided it was worth paying for a good internet security suite.

Hopefully the deep scan will get it -
but you can also download & run SUPERAntiSpyware- sometimes one will get what the other misses.
http://www.superantispyware.com/

And
Did you try the
CCCleaner (free edition) = http://www.piriform.com/ccleaner/download

I use it also - just leave all the settings as they come, don't change anything, and you won't have to worry about the wrong thing being cleaned or removed.