20:48:53: Total frames encoded: 47255, total frames duplicated: 1015 (2.15%)
20:48:53: Number of frames skipped due to encoder lag: 46 (0.10%)
20:48:53: Total frames rendered: 47159, number of late frames: 107 (0.23%) (it's okay for some frames to be late)
Your CPU isn't quite able to capture 1080p60 on UltraFast, as evidenced by the > 2% duplicated frames. You have a GTX 960, so you should be able to try NVEnc recording instead. Change the bitrate to 25,000 or so and use the NVEnc option. Also you can change your keyframe interval to auto for either setup.
20:39:32: WARNING: Another hook is already present while trying to hook d3d9.dll, hook target is unknown. If you experience crashes, try disabling the other hooking application
Does look better, but still 3-4% duplicated frames. Worried about this message in the logs:
But I'm not familiar with how to best game capture CS:GO. Might do some forum searches on that. Or maybe someone else can look at it. If not I'd try cutting the frame rate to 30fps next, but I think that won't help much because the bottleneck is in the capture method.
Been having the exact same issue for about a week and haven't been able to fix it at all!