I just upgraded from 6.0.1608.10 to 6.1.1611.25. On .mp4 files, I'm having some significant problems:
1) The output file now seems to have far fewer K frames (I'm guessing) than 6.0 produced. When I open the output file in Media Player Classic Home Cinema or VLC, and try to position somewhere in the middle of the file, it often sits there for 10 seconds with the timer counting up, before it finally begins to show the video. In the older version, I could position around at will, and the proper video would appear within a fraction of a second. I've gone back to the 6.0 version (which unfortunately resurrects some other bugs), and redid the same videos, and the results are fine now.
2) When moving around in the timeline, in 6.1 I often see a gray "ghost" image, as if there was no K frame available, so it tried to apply the relative frame on top of a solid gray frame. This never seems to appear in the resulting output file, though, but I suspect it's related to problem 1.
3) When I open a file in the timeline, it takes a loooooong time for the thumbnails to appear. Sometimes, it takes ten or twenty seconds between thumbnails, during which time the CPU usage is zero. In 6.0, they appear at a rate of about one per second (on a fast machine).
It looks like something major has changed in the algorithm for generating the output file, at least for .mp4 files, and it's buggy. In the meantime, I'm sticking to 6.0.