I've been using 7+ Taskbar Tweaker for a long time without any problems but recently I've been having the one I'm about to describe, it may have something to do with Office 2013. I use Excel quite a lot and constantly open and close different worksheets. There are some which I always have open so I like to have them arranged in a specific sequence. When I was using Office 2010 I never had this problem but now from time to time grouped items will rearrange themselves. Unfortunately I can't spot when exactly it happens or whether I do something specific. I know the major change between Excel 2010 and 2013 which I like a lot is that Excel windows are now independent which solves all alt+tab problems among other things. Maybe this has something to do? I tried disabling grouping by Application ID and then the problem doesn't seem to occur but this doesn't work for me so I didn't test it for very long.
Customer support service by UserEcho