My main action bar is normally something like 22 buttons and is more or less centred on the screen horizontally. With 1.01 my action bar is 52 buttons and extends all the way to the left side (and maybe further) and the icons seem to be wrapping around (same actions show up in the bar multiple times).

It seems like the migration errored out the first time, and upon logging in again it finally completed, thus setting your DBversion to 1.3. The error was that the migration script errored out the first time, the fact that you have extra buttons is actually per the script to make sure you didn't lose any data.

The solution is to just remove the extra buttons from the bars that you don't need. Just open the bar editor and change the size back to what it should be.

Data migrations are never smooth, and this one is following in the same vein. Though the database is finally how it should be going forward now, so this is the last time you'll ever have an issue like this