Possible reasons why the negative PCR studies on XMRV came up negative

DZ: When a new study, like Peterson's, comes out, look carefully - did they prove their assay can detect viral nucleic acid that has been integrated into DNA or otherwise subjected to the unique environment of a human body? In other words, has their assay been clinically validated? If not, and they found little or nothing, one really cannot be sure that their assay works on human samples at all.

Check out The IMEA (International ME Association): PCR and HGRVs: The challenges:

HGRVs cannot replicate in resting cells. They integrate into host DNA. XMRV (one variant of HGRV) integrates preferentially into CpG islands which have a huge c-g content and hence are an example of the complex secondary structures discussed below. HGRVs also exist in amethylated state and as such are very prone to oxidative stress. This either leads to mispriming, mismatches or reduces the binding strength between complimentary bases. Therefore, PCR faces completely different challenges in this environment than it does when being used to locate a non integrated naked clone in a spiked sample. Read more>>