AC - The paper has been rejected once so far. I won't mention the journal, but it was rejected on an editorial basis before it reached the peer review stage. I can only conjecture regarding why the editor decided to pass on the paper, but it was not (to my knowledge) rejected for any methodological deficiencies. We are currently in the review stage at a second journal and the reviewers had no trouble with our methods, only how we argue for multiple comparisons correction without stepping on too many toes.
As an interesting aside, the poster was also rejected at first. All the peer reviewers thought is was a joke and voted to exclude it from the conference. Once it went before the program committee they realized that, even though we had an odd approach, the conclusions of our data were sound and that we had a very good point to make.