I don't know of any documentation on this issue. There's one more thing we did which I forgot to mention, and that was under the 'WindowsMobile' folder (under ContentRoot). I had issues with pathing, and even though these fixes would eventually work, we needed to remove all records of past projects in the sub folder off of 'WindowMobile', in my case, a folder I had named 'Traffic'. After that everything worked.
Chris O. at ESRI also mentioned that adding 'db_owner' to the soc account in SQL has helped a person in the past. This wasn't needed in my situation, but you might want to check that for your setup.
Are you able to bring in a service to MPC from your web server and then save it to the web server? If you can and these changes haven't worked yet, you might want to clear that folder out and try again. Strangely enough this was one of the magic bullets.
I've also noticed that if you change the pooling to a service before you work in MPC, it sometimes will not show up when added? I went back, changed the service to 'Pooling', went back to MPC and viola. oddly this hasn't happened every time. So after you make your map in MPC, you can just go back to the AGS manager and change the pooling of the service to 'Not Pooled'.