I received some feedback, which you may haved been plagued with and I wanted to make sure that all knew of this issue too. At its heart TotalEdit uses a third party library, which manages visual part of the application including the tool bars, docked windows and the customisable features such as the keyboard mapping. It turns out that unlike all other user settings being saved to file any edits to the keyboard shortcuts are not. They are currently being saved to the registry, which the installer resets during the upgrade.
I tried backing up the keyboard changes before an upgrade and restoring them afterward but this failed. I am now trying to work out a solution so that users' do not have to re-setup any customised keyboard mappings. Plus I will look to see how I can save the settings to file just as the other settings are.
Apologies for the issues that this will cause. Hopefully a solution will be found shortly.