First, besides this small hiccup, this plugin has been wonderful! I highly suggest it for those bleeding edge folks.
So the issue was that I was jumping from 3.0 Beta 1 to the most recent nightly, 3.0 RC3-15260. It put up the maintenance message while in the backend. As I was doing triage and backing up the all important config, htaccess, and wp-content files/directories, I noticed ".maintenance" sitting around on my server. On a whim, I deleted it and my site was restored and, according to the footer message in the backend, I had successfully been upgraded.
I tried a test post without any issue and everything else seems to be just fine.
I'm assuming the .maintenance file simply got stuck?