Hm, well it does seem to be different in your videos, which is interesting. The original version of OBS just basically changes a single encoder setting, the frame playback and framerate is still completely unchanged even in that version, so maybe that encoder setting does something that makes it decode differently. I could throw that setting in to OBS MP as well, I suppose it would be no harm. Thank you for the videos, though. I should investigate this further to see if that encoder setting is indeed causing a difference.
By the way, do you have enough space on your hard drive to test out lossless recording? Maybe you could test this in FFmpeg recording output with huffyuv encoding on an AVI file and see what results you get there. It'll be a huge recording file so you probably can't record longer than you've already recorded. It'll eat up gigs in no time, but may be worth the test. (Oh wait, might not want to do this on an SSD though, fair warning)