This happens for me as well and started immediately after the Windows 10 Creator Update.
I have tick-boxes enabled for my icons, so I do know if I clicked them or not. Double-clicking an icon sometimes (but not always) does a hide on a desktop even though it got ticked with the first click. The mouse pointer is definitely over the icon.
Also seeing a delay with double-clicks when applications do open, maybe 1 or 2 seconds before anything happens. That is the same for any icon, including This PC and was previously much quicker. If I double-click that same icon through an Explorer window then it is instant, so it does appear to be a desktop / Fences related issue.
I've turned off the show/hide option because that issue is extremely annoying. That does not have any effect on the delay.