Yup. If anyone gives a rat's, I do upgrades like this:
1/ Get the large upgrade for the version I'm currently using, and load all files except the upgrade php and sql files.
2/ Delete all mod zips.
3/ Uninstall and delete all custom themes.
4/ At this point you effectively have a new, vanilla installation. Then
upload all the large upgrade files for the new version (including the actual php and sql upgrade scripts)
5/ Run upgrade.
6/ Install custom stuffs.
7/ Have beer.
Works perfectly every time.