This is an old post but seems like a good place for my first post.
I had this happen to me. I did a number of things to resolve the problem. First I clean my primers. Then I personally wash all tips/tubes/plates etc (by plates I don't mean the 384 well one only 96). And I used Q-PCR mixtures that only I had used (can't trust everyone else is as careful as you may be). I used Milli-Q water and if I didn't get new water and storage bottle regularly there tended to be more noise due to contamination.
Hope this is some help.
