how to overcome primer contamination - need protocol (Jun/01/2011 )

It was a phage T7 gene. We did also try a number of different polymerases. The fact is that at first we didn't observe anything in the no template control. Only after a few months of qPCR work with the same amplicon did things start to get messy.

I have similar "contamination" problems. Do you think that if I use the relative quantities of the unknown samples and find that they are 100 or more times higher than the controls, I can use my results?
Or if the Ct value difference between the unknown samples and the controls is bigger than 6-7 cycles?