I'm suspicious of the implication that upgrading the system somehow caused
the problem, while a fresh reinstall would not. Luckily, you've kept all the
pieces you need to test your theory. Just put back in the drive with the
flaky system, and upgrade it to the same version of Ubuntu that you freshly
If the upgraded system remains flaky, you can investigate further, perhaps
diff the two drives to find the "cobweb" that the upgrade left. And file a
bug report or whatever.
If the upgraded system is as solid as the reinstalled one, you'll know that
a) your superstition about upgrades is not holding much water and b) the
problem was actually fixed by a new version of the kernel/X/whatever.