Hello,
First, and most immmediately, I have the same problem. I have seven screens. The Fences are all in the correct places but the icons were all overlapping on my "Startup" page. As far as I could make out, they were in the positions that previously they had occupied on their separate pages. This has been the case for two days. When, today, I tried reverting to a backup the icons/links that I had created in the past week all appeared in their appropriate locations but everything else was clustered at the bottom right of the "Startup" page.
I seem to recall that I had responded to an invitation to update something Stardock but I cannot now recall whether it was "Fences" or "Start11". Certainly, my systematic ordering of programs on the taskbar had been jumbled up.
In the past, this overlap issue has occurred briefly on some boots but has then sorted itself out within 20 seconds or so.
If there is no 'magic wand' solution, to reposition hundreds of icons is going to consume a lot of valuable time.
Second, I have been meaning to raise the issue that it looks to me that what gets backed up is only the startup page, not any other pages that have been created.
Third, having been precipitated into contacting you because of the first and really serious problem I'll also take the opportunity to raise the matter of another, more minor, annoyance. I'm running a fast machine but there is a noticeable delay between the creation of a link and its appearance. When it does appear it can be recalcitrant in that it cannot always be made to move with the mouse to where I want it to be located. Also, once moved to the desired location for a while it retains attention in the form of the marker around the icon and cannot always be made to drop it simply by clicking elsewhere.
I use "Fences", "Start" and "Groupy" on a daily basis and they are fundamental to how I organise my research and how I write. The sort of customisation that they make possible is essential for anyone who aims to be efficient in their research. By far the most important of these is "Fences", but sometimes it can be rather flakey. I've lived with this, but the first of the problems that I report here goes beyond `flakey'.