Part of the problem seems to be solved, after quite extensive googling.
It seems that LR 6.3 actually has a bug in handling of video fileformats. There exists a fix that I found from another forum (Lightoom 6.3: After update I can't open any video files). Interestingly enough, this solved my problem, even when my LR 6.3 reported to be "up to date". Solution is to replace video related dll-file in Lightroom folder, as per instructions from Adobe kb (Error "Sequencer defunct" when using video file related functions).
Now it seems that catalog sync goes smoothly again.
Thank you for your insight.
The main problem that I had was not with playing the files, but the fact that import hang when ever folder did contain video file. No preview was rendered for video files, and when attempting to import hang resulted. Also, some times when video file was present the import dialog started to list much higher number of files than was included in the directory.
The Adobe kb solution linked in my previous post did fix the problem.
I also installed the said dll file and thought the problem was solved because it went away. But then I had the same problem again 3 days later and then I deleted the videochach's content. Since then all is good.
Thank you for adding this, its very good to know just in case the issue re-appears.