So often, to get good playback it's useful to transcode to an intraframe codec, or at least to a long-GOP format with less extreme use of things like partial i-frames and long picture 'groups'. Handbrake can do that to an easier to process form of H.264, and you missed the capability of that app to batch process, which it does do. There are online files and the help for Handbrake that do cover the process.