I also have this problem and have been working with Apple support to try to resolve it. For me it happens whenever:
- I try to take an app to full-screen mode
- I try to animate between Desktop Spaces using the mouse (two-finger swipe), trackpad, keyboard commands, or anything else that causes the Desktop Space to switch.
- I watch a video in full-screen mode
I think the unifying thing here is the automatic switching to a different Desktop Space, including for full-screen. Interestingly, if I navigate Desktop Spaces manually, usuing Mission Control, I'm successful in switching.
Of note, this is only affecting my account. I created a "test" account and everything works fine. Apple thinks it's something that's loading during my unique login and we're working on isolating the problem.
If (when) I get a resolution from Apple, I will post here. BTW, you may want to create a "test" account and try going to full-screen mode with an app, and navigating spaces. If it works, you've isolated the problem to some idiosyncracy in your account.
I posted a similar response on this thread---sierra full screen bug---which appears to describe a similar problem.
BTW, I've already performed the reset SMC, NVRAM, and PRAM, as well as numerous other "system" fixes, without result. If I get a solution from Apple (we're supposed to talk again on Monday), I will post it.