When updating to 2.3.1 from 2.2.1 I ran into problems with the new wp_terms tables not being created. The updater reports back OK but it has not created these new tables. At the very least, the updater should report any errors in the modifications it is attempting to perform. The 2.3 updater reported back that it was successful when it clearly was not.
I suspect that the problem may have been due to a plugin that was not disabled before modification but there again, the updater could probably check the status of plugins and either refuse to run or advise the user to follow directions more carefully.