As I said on another post there's iTop easy desk which does most of what Fences does and it's free. I didn't go to it the first time I had to rearrange the desktop but I may now.
I suspect you promote another (inferior) product in our forums because you believe it will motivate us to act differently or change a design course. It does not. Client experience and satisfaction, however, do.
I also am having exactly the same problem. On any restart or login the Fences have moved mostly to the left end of my wide screen. They're on top of each other and half the icons are out of Fences. I've re-installed Fences and no improvement. At least I've been able to go back to a saved screen BUT now I can't every saved screen comes up with the same problem. I have way too many icons on my desktop and Fences hides them nicely but when it's not working my desktop's a mess, re-arranging them back to Fences is about a half day chore and this is my 2nd time the backups didn't work. This may seem a small deal but with a 34" screen (3440 x 1440) there's a big mess. At this point I don't know if it's worth doing it again
When someone installs Fences 5.53 with a prior version of Fences 5 already installed, it will keep the Fence 'layout' option they had. Most have 'Store my Fence group positions on a per-screen-resolution basis'

While we need to know if that process - keeping the old setting - is causing issues, we have repeatedly asked clients experiencing issues to set it to 'Store my layouts on a per-monitor-configuration basis.

While there may be a need to adjust Fences thereafter, we very much want to know if that solves your issue long-term (post multiple reboots and under multiple monitor configurations). This is detailed more here
https://forums.stardock.com/528046/get;3931457
Lastly, with that option set, upon reboot, there may indeed be a short delay between when the desktop is rendered and when Fences does its thing (arranges the desktop). In other words, if you reboot and things do not immediately seem correct, give it a few seconds before suspecting something is wrong.
The reason for this, Fences wants to ensure that the desktop (on all monitors), is fully started before it acts on it.
Note to moderators: Please keep me informed of what they have set when reported and their results from doing this process.
Sean Drohan
Stardock Product Lifecycle Manager