dropping frames with 1 144hz and 1 60hz monitor

I've been having issues with this for quite some time and while I've found people with similar problems, I've never found a good answer.

My issue is this:
I have a 144hz and a 60hz monitor, and I'm unable to run things in borderless windowed without having stuttering/dropped frames. Disabling Aero has helped to a certain extent, but I'm unable to use Nvidia shadowplay to capture instant replays with it disabled. (I'd ideally like to be able to capture matches I've just played in Tekken 7 at will)

I've also tried putting the secondary monitor on the integrated GPU, but that seems to make the issue even worse.

Setup:
Gigabyte Z170 UD5
16GB DDR4 3000
GTX 1080 FE
i7-6700K
Windows 7 64 bit

I was never able to find a solution to this.

Having gsync enabled seem to fix the problem in most cases, but not all.

My 100% fix was to replace my 60hz monitor with a 144hz monitor.

That's kind of what I was hoping I wouldn't have to do, but so far I haven't found any other real way around it.

I have an identical setup. 1080Ti with a 144hz and 60hz panels. My 144hz is gsync but I’ve always run in full screen mode and never experienced this problem. May need to do windowed and see if I get the same results as you.

I have the same set up as you and i have noticed weird things with Frames espically with videos loading on my 60hz screen. I will be replacing it with another gsync 144 screen this week so maybe some stuff will be gone.