I bet this is not a very original thread but...
I started having contamination a few months ago while I was working on another project dealing with plant microsats (before that, never had any issue with PCR).
Now I am back to my own project (microbial stuff) and I still have contamination (the negative control of my PCR is positive while it only contains mastermix). The band is at 1.5kb (bacterial 16S).
In between the two projects, I cleaned the whole lab, bleached the pipettes, benches, etc...Plus, I do not use the same chemicals. The contamination seems random (ie if I prepare several negative controls some will have a band, others won't).
What else can I say ?
Please ask for more informations !