What a coincidence, I've been having the same issue ever since I upgraded Fences Pro. I believe I have version 3.09 and my records indicate I upgraded on 1-19-2020. I have Windows 10 version 21H1 Build 19043.1889. I just today purchased the upgrade to 4.0 but as of this writing have not installed it. I was not aware of the 4.0 upgrade so maybe the issues will go away, maybe they won't, when I do the upgrade.
I have dual monitors if that matters, and it seems to happen if I have multiple applications open. There are no specific applications that cause the problem. There are no error messages. No particular pattern that I can see, but as the OP said, it will fix itself eventually. This never happened prior to the 3.09 upgrade.
This morning I installed a new video card, an EVGA GTX1650 Super, 4GB. The reason I am even here now is because I noticed that a number of icons inside the fences were jumbled around AFTER I had installed the card but before I updated the driver. Why that happened I have no idea but I was starting get very disenchanted with Fences. The fences themselves were not moved, just the icons inside them, and they stayed within the Fence.