Yep, I'm rewriting the check for Kindle connected and the customization pre-checks to be a lot more thorough and correct. Unfortunately when I made the error dialogs nicer for the Menu customization entry, it broke the customization invoked by the Preferences dialog. (See the separate thread about do_user_config - I was trying to avoid the large window created when there wasn't anything to customize, but only fixed it in one area).
I do have some more information on where collections come from in the debug output - but I might be able to append it to the report. Debug shouldn't need to be run unless there is an unexpected issue.