Have you done a good check for malware?
Typically, there are system issues after infected users think they have "removed" the malware. The malware may be gone, but some residual system effects may remain.
Just to be safe...and to get advice/suggestions from those who normally deal with malware situations and the aftermath...I suggest posting at BleepingComputer.com - Am I infected What do I do - http://www.bleepingcomputer.com/forums/f/103/am-i-infected-what-do-i-do/
If you've already done such, it helps to know that.