There has been a few blog posts about how to fix your Master Data Services if you've on some stage had SQL Server 2008 R2 installed. This can be fixed by copying certain dll from folder to folder as James Serra, a friend of mine has just written.
I actually experienced similar issue few months ago and just didn't have time to investigate what was wrong with it. So I ended up installing another instance to fresh virtual machine. After I noticed James's article I tried the fix but it just didn't work for me. I never had 2008 R2 installed on that virtual machine so it just wasn't because of that.
After turning on the trace logging I noticed that my errors were a bit different.
MDS Error: 0 : Service started successfully, Assembly version: 126.96.36.199, file version: 11.0.2218.0 ((SQL11_RTM_GDR).120612-1251 ) DateTime=2013-01-03T17:11:25.1111983Z
MDS Error: 0 : ApiContractVersion: 5102 DateTime=2013-01-03T17:11:25.1111983Z
MDS Start: 1 : Service.InitializeExpirationStatus DateTime=2013-01-03T17:11:25.1111983Z
MDS Information: 0 : Evaluation period days remaining code: 4294967040 DateTime=2013-01-03T17:11:26.0799607Z
MDS Error: 0 : LogError : The Microsoft SQL Server license has expired. DateTime=2013-01-03T17:11:26.0799607Z
It pretty much says that evaluation period has ended. This is actually because I've firstly installed some pre-release version of SQL Server 2012 on that machine and done an in-place upgrade to RTM when it was released. I know that it wasn't officially supported so I'm on my own here. After setting up call-stack monitoring I noticed that when MDS application pool does its ExpirationStatus check it will read from registry at: HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\110\Master Data Services\Setup
At the server which was upgraded from CTP the registry folder was (I've blurred checksum because I'm not sure if it has something to do with my personal licence):
And at the server which has a clean install the registry folder was:
CTP upgraded version has Edition as "Enterprise Evaluation Edition" and it is missing some of the keys as well as one additional folder.
I exported the keys from the server with clean install and imported them to CTP in-place upgraded server and after recycling the IIS:
I hope that this with James's article will help you if you encounter such problems.