To keep Spybot from removing MFU from now on,you can open Spybot start center,checkmark Advanced User Mode,click Settings,click the Categories tab,and somewhere within the Categories window,rightclick and select Spyware Scan Only,then click Apply and OK.That should prevent Spybot from scanning for tracks,including MFU programs:
http://www.safer-networking.org/faq/usage-tracks/
I'm not sure why mfu programs weren't recovered from Quarantine,but the list should repopulate as you use your programs over time.