So, these papers (December 21st, 2001, Retrovirology) that have been published don't refute the fact that XMRV exists as a virus. They don't challenge the previously positive studies.
All they say is that you have to be careful that when you are testing for XMRV using PCR that you don't have any mouse DNA contaminating things, because if you do, you can come to the wrong conclusion.
I would also point out that there are a lot of other studies, many of which are published, some of which aren't. These studies used other standard virological methods which are not PCR-based, that have found XMRV in patients.
So, if you go back to the original Science paper that showed the presence of XMRV in patients with chronic fatigue syndrome, you'll find there were five different methods used, four of which are not PCR-based.
So, that was what was lost in the publicity of these papers in Retrovirology. Read the Interview: Dr. Eric Klein of the Cleveland Clinic Talks about XMRV Research