Have just performed a 3.4.2 -> 3.5.1 network update.
This invoked a dbDelta call, trying to re-create users, usermeta and blogs:
This happened for every blog/site in the network.
It may have tried more tables, but the error is truncated.
Yes, there were lots of plugins activated, yes it is a custom theme, and no I haven't managed to isolate it to find out if it really is a core problem.
I'm putting this here for reference, in case someone else sees the same problem.
Not found any fallout yet from the errors.