I've been having this same issue as well. It only happens with certain games, and with some testing, it only happens when OBS is on another monitor? (might be because 1/4 the monitor was covered by OBS being Always on Top).
OBS Log w/ 2 different recording:
https://gist.github.com/Drewlinskii/3a9e2bdc4cbad3d2bedd99da56ef6099
Recording 1:
https://youtu.be/WG8mICQouqk
Recording 2:
https://youtu.be/2wH-XajHvk0
GPUz:
http://gpuz.techpowerup.com/17/06/24/wx6.png
Games I've had this same issue with: Euro Truck Simulator 2, American Truck Simulator 2, Tomb Raider, Rise of the Tomb Raider (all I can think of atm).
The FPS counter on the bottom right corner will just drop down in the 50s and even 40s at times, while the game is still looking pretty decent w/ no major FPS drop (in game). I can visually see in the OBS preview that the frames look MUCH worse than what I'm seeing on my main monitor, and viewers will point out that they experience horrific frame drops when OBS' FPS is dropping.
I just want to know why this happens and help fix the issue, whether it's an issue on my end, or on OBS.