If it changed, then there would have been more time than a month between time it was pulled or put into further review and the time it was approved for publication again. If suddenly it changes the whole conclusion, then they would surely be gunshy about publishing it. The timing supports just a few more tests to confirm the conclusion already in the paper. In fact, if something changed, then I would think publishers would maybe not want to publish it at all.
If that is the case, then we can expect the results to be even stronger with the additional effort in the last month.
I also don't think CDC can influence Alter. He seems to be a big boy and not subject to intimidation from CDC. Pulling it temporary is insult enough, but understandable. I guess what I am saying is this is not Defreitas. Alter and the other author are too prominent and confident, in a respected government agency on their own, to allow CDC to stop publication of their paper.
Plus, there have been lots of leaks to news media. The hold back of both papers were leaked. If pressure caused change in FDA results, surely this would also be leaked. But Mindy, who says she has sources, says the results are the same.
Another point, there is a public health issue here. I would think that if FDA / NIH was getting pressure to quash the study, or if CDC was bullying them to keep quiet, then for the sake of public health, especially someone whose job is to protect safety of blood supply, they would be slipping copies of e-mails to every news media that would accept it.
Let's just wait and see.
Remember, this controversy is not unusual; AIDS story is similar.
Take comfort that many, many scientists and at least one drug company are looking into XMRV completely independent of CDC, FDA and NIH. It takes time, but the truth will come out. We also have WPI, NCI and CC squarely on our side. And the last two have solid reputations. CDC does not hold all the power. In fact, most discoveries in the last twenty years had nothing to do with CDC. I looked, only major discovery they have had in last 20 years was West Nile Virus.