SQL Server 2012 Always On AG - DBEngine Service account locking
So just in case someone wants to know what caused this, It was a group policy!

Some time ago, unbeknown to me, the domain controllers for the domain in question had been upgraded to Server 2012. Along with this came a whole bunch of Windows Server 2012 group policies. Additional policies had been added to one of the parent server OU's with a filter applied. 

Unfortunately the filter had a typo, and so it was being applied to all of my database servers on this domain.

I had almost ruled out it being a GP issue, as I seemed to have all the permissions I needed, and I could see connections coming in on the correct ports between each node. The servers were happily running as single nodes!

I asked the server team to move the servers (just to see) to the 'computers' OU, and after a forced gpupdate, bingo! 

Unfortunately, I am unsure exactly which policy caused the problem as there were a lot! There was a number to do with NTLM usage and authentication, and I'm convinced the issue was related to this. I will at some point set up a test lab to try and replicate the issue.

So there you go! Always check group policies, even if you believe (like I did) that nothing had changed!