Actually, this is not uncommon. To us, the computer is not doing anything, but it is ALWAYS doing a task or two.
Some of the trojans, viri and malware are self replicating which means they make little "baby" ones.
Once you clean out the Temp files, Cache, Cookies and such, then run a good antispyware program, you should be ok.
As for the VPS database.....
the new detections could be the result of the updated signature files, but most likely you still have leftover junk that you need to clean out.
Regularly running a full AV scan, AntiSpyware scan and a good Anti-Trojan scanner like A-Squared (A-2) will keep most troublesome "invaders" out of your system.
There is no magic answer here. It will take some time and effort to get your system "bug" free, but it can....and will be done.
Talk to you when you have accomplished the tasks outlined here.
Good luck.