12:41:58.909: Output 'adv_file_output': Number of lagged frames due to rendering lag/stalls: 119 (17.7%)
12:43:06.598: Output 'adv_file_output': Number of lagged frames due to rendering lag/stalls: 354 (19.5%)
12:44:23.940: Output 'adv_file_output': Number of lagged frames due to rendering lag/stalls: 162 (15.4%)
12:45:58.522: Output 'adv_file_output': Number of lagged frames due to rendering lag/stalls: 192 (18.2%)
The problem is you have rendering lag caused by overloading your GPU, but all your adjustments are to your encoding settings, and it's not those settings that are causing the problem.
Basically running your game at 90 FPS is loading the GPU so much that OBS can't run. About 15-20% of the time, when OBS wants to render a frame before encoding it, it can't because the GPU is too busy running the game. So OBS duplicates the last good frame and encodes it, and you get visible stutter.
You need to change settings to reduce GPU load. This could be one or more of the following changes:
- Capture either 720p60 or 1080p30 rather than 1080p60;
- Cap framerate in game
- Activate vsync
- Change graphical quality settings in your game to reduce GPU load