What did you do, specifically? Backup -> Move -> Update -> Test?

Backup -> Move -> Test -> Update -> Test

With the results being the same either way. The previous install was @ 6a035d977f22aaf1 (I will admit this was a bit lazy.. that's from November of last year).

The other thing that's probably worth mentioning is that when I tried to create a new repo on the updated install, it has the same problems. Running the failing command in the repository root also succeeds, so it seems to be a paths thing... although the '.git' at the end of the command freaks me out, because the repos are bare, so there is no .git folder.