Whole lab experiencing inconsistent PCR contamination - (Feb/05/2013 )

How close is the PCR preparation area and the gel area? If the room is not well ventilated and you ran the gel close to the PCR preparation - you may have some of the PCR fragments just flying around.

We had similar problem in our lab, and now we prepare PCR/qPCR in separate room, and runing gels in other lab (even changing lab coats) in 2 years we had only few cases of negative control giving a band.

Hope it helps somehow..