I'm very happy to say that after spending almost 5 hours trying to fix this exact same issue for one of my clients I came across this post. The information provided by nrgadmin has helped me resolve the issue and I have a working BES server again.
I had just about given up on it, and I read the advice regarding Microsoft Patch KB980232. The strange thing is that this server had that patch installed several months prior to this issue arising which is bizarre.
I followed the steps by removing the patch, rebooting, then installing all outstanding patches from Microsoft Update, including KB980232. Everything just started working again.
One difference to nrgadmin in my case was the the "net view" command was working fine. However the command "sc \\127.0.0.1 query" would return an error saying that the "RPC Server was unavailable". Checking on several other servers that didn't have issues, that "sc" command worked fine. As soon as KB980232 was removed, then re-installed with the other patches the "sc" command worked as expected and produced a large amount of output about the services on the box.
KB980232 is a patch for the SMB Client as nrgadmin stated. There is obviously something going on deep inside the networking stack that breaks something to do with NetBIOS listening on the localhost IP. But I'm not prepared to spend another day researching it at this stage.
Also worth noting is we came across another issue at a completely different site a few days later. A Multi-Function printer/scanner had all of a sudden lost the ability to save files to a server that had been working for over 12 months prior. I suspected a similar problem, and sure enough when I tested with the "sc \\127.0.0.1 query" command I received the same RPC error. I applied the same method as recommended by nrgadmin (remove KB980232, reboot, re-install all patches) and the problem was solved!
So I'd just like to say a big thanks to nrgadmin