I wouldn't rule out bacteria. PT Nuke won't kill everything. There's even bacteria that lives in diesel. Do you have any silver in the loop? Is the res open or closed now? Pics would help.
Depending on what blocks you're using, you may have to take it apart as the fins can be very fine and will have lots of deposits that'll need to be physically brushed out. Boiling and vinegar alone won't do it.
http://img146.imageshack.us/img146/1143/dsc00422qc.jpg