Using two monitors, one widescreen monitor and one vertically oriented monitor. The widescreen monitor is using a custom fancy zone layout while the vertical monitor is using the
"Rows" layout (see all monitor screenshot below).
Windows build number: Microsoft Windows [Version 10.0.18362.778]
PowerToys version: v0.16.1
PowerToy module for which you are reporting the bug (if applicable): Fancy Zones


I've encountered the same problem. When I originally configured the feature, it worked fine across both monitors. Single zone-layout per monitor was displayed. But as I changed physical screens (e.g. swapping monitors) and changing connections (e.g. swapping USB input to HDMI and HDMI to DisplayPort) I encountered the several overlapping zones problem as explained above.
Guessing, it looks like FanzyZones is overlaying the prior zone layouts that had been used with the monitor all at the same time vs only using the currently active layout. Turning off the "show zones on all monitors" feature fixes the multiple-zone-layouts-displayed-on-a-single-monitor problem.
Edit: killing the PowerToys process and relaunching PowerToys seems to have fixed the multi-layouts-overlay problem. I re-enabled the "show zones on all monitors" feature and is working as expected. I'll update this note if the feature starts to cause problems again.
It was fixed here when doing following:
Note: First I wanted to write that the issue occurred when doing these steps; but when trying to reproduce it, fixed the issue.
I had the same problem - there were at least three layers of zones appearing for me (I use two monitors, though I have had a tablet connected as a third a while ago)
Restarting PowerToys seemed to make it go back to normal this time

I had this happen again today - the fancy zones were under the start menu. Restarting PowerToys fixed it again.
It's possibly related to the screen geometry changing when docking/undocking from external monitor - my Laptop always seems to get into a bit of a confused state each morning waking from hibernation, and bounces windows between montitors as it tries to decide which one is primary.
Edit:
Ok, now I have repro steps (for my machine, anyway)
Task bar on left of screen on both displays
Unplug USB dock cable. Wait for everything to settle down
I've found it's also fixed by just toggling FancyZones off and on again.
I'm guessing the simplest fix would be to detect that the desktop/screen layout has changed, and just reset the module
I think that the #4694 fix has fixed this one, too
@benjymous
yes, it may have fixed it.
@fwdsimonp
can you check if it still repros using 0.19.2? https://github.com/microsoft/PowerToys/releases/tag/v0.19.2
Thanks.
@enricogior So far, so good. I did a bit of testing and have not seen the issue. If it does come back, then I'll update here.
@fwdsimonp
thanks for the feedback, I'll close it for now, feel free to reopen if it comes back.
Thanks.