Solved it, and it is a corker. I thought I had tried everything, but then I checked the databases on (localdb)\v11.0 in SQL Management Studio, and discovered they were readonly... and then the penny dropped.... the samples are installed in Program Files by the 4.5.30 installer. As soon as I granted the Users group on my PC write full priveleges to the samples directory it all worked fine.
Edit: Thinking about this logically, the issue must be that the user account SQL Express is running in doesn't have permissions to write to Program Files.
Absolutely no indication of anything like that in the error messages returned by any part of .net of course. Hopefully the above will save others some pain.
Edit 2: I have now fully documented everything I did to ProjectTracker running in VS2013 here: http://forums.lhotka.net/forums/t/12200.aspx.