I got the same problem. Been trying to fix it forever. 144hz with 60hz. Im not completely sure if its an issue only with windows 10. But i really don't remembering having this issue when i used w7 like a year ago.
Tried testing it with virtual machines, but doesn't seems to have an effect. So next step is installing windows 7 on an additional disk and boot it up from that one.
Try doing a test:
Put this on your main 144hz monitor:
http://www.testufo.com/#test=frameratesPut something like a youtube video on your 60hz.
See if the stutter happens when the video is running. Then try closing everything on the 60hz and see if the framerate gets stable again.
This post was edited by ZwiX on Sep 26 2016 01:20am