Ok, finally found the problem (tail between my legs). I made a stupid error in my config and forgot to point to the map server on the new server and left it pointing to our old server, thus no errors. Of course I didn't see edits made on the new server. DOH!
So, everything is working as advertised. I do still think the new publishing routine is a pain in the rear but all the blame for this issue lands squarely to myself, not ESRI.
Thanks, ESRI