Update (6/19/14): The folks at JNCI and OUP have kindly confirmed that they will consider manuscripts that have been posted to preprint servers.
I just got this email about a paper we submitted to JNCI
Dear Dr. Leek:
I am sorry that we will not be able to use the above-titled manuscript. Unfortunately, the paper was published online on a site called bioRXiv, The Preprint Server for Biology, hosted by Cold Spring Harbor Lab. JNCI does not publish previously published work.
Thank you for your submission to the Journal.
I have to say I’m not totally surprised, but I am a little disappointed, the future of academic publishing is definitely not evenly distributed.