It sounds like it maybe skipped a step, possibly during the timeout. Basically what it is supposed to do is run through each of the altertables needed to get you from your old version to the new one. In your case it should have only run the 7.1 altertable.
It's definitely odd that it took that long as there aren't really any heavy database queries in the upgrade. What I'd do is during the upgrade, run the "mysqladmin processlist" command from time to time, this will tell you exactly what it's doing.
