1) FREESYNC ON or OFF (need an R9-200 series or newer AMD card)?
2) Just FYI, but in FREESYNC MODE you only support up to 90Hz (90FPS). I don't know if it just caps to that, or if it defaults to VSYNC OFF or VSYNC ON above 90FPS.
If it doesn't cap, then I'd set a global cap or cap each game manually.
3) this guy had a similar problem:
http://www.overclock.net/t/1565932/asus-mg279q-stuck-at-60hz-on-some-games-and-other-issues
"I was also able to select 90hz at 1440P after first setting 60hz in Diablo 3 in non-freesync mode, and then exiting the game, enabling freesync via the monitor controls, and finally re-launching Diablo 3. This allowed me to select 1440P at 90Hz and has been running great ever since."
4) if it's an NVidia card no Freesync, but I would then consider capping games to 72FPS by doing this:
a) start then close game, then
b) NCP-> manage 3d settings-> ... add game-> adaptive VSYNC (half refresh)-> SAVE settings
Set game quality so it stays at 72FPS at least 90% of the time, and drops the other 10% or less (which will auto disable VSYNC so not added stutter but you get screen tear)
5) Reboot?
No idea why that is, but that is very odd because I've never needed to do that for any video card.
Did you try just changing the refresh rate back to 144Hz?