I was just dealing with this. In my case is was 1080i wtv files created by Windows Media Center. I solved the choppy video and audio sync problem by turning the setting "Sync playback to display" ON. I was connected to a 1920x1080 monitor by HDMI. I'm still have a problem with these files, but now it is limited to the audio where I get cracks and pops while playing the file. The audio connection is analog to an external speaker The video is however smooth and the audio is in sync. I had no problems, before or after, with 720p wtv files or H264 and H265 1080p video files. I'm at a loss at this point and might try to install Kodi under Raspian to compare. Any help would be appreciated.