It may help to have 1080p 60/59.94/50/24/23.976 modes whitelisted and adjust refresh start/stop enabled as it will eliminate or greatly reduce the amount of correction Kodi needs to attempt; as the decoder doesn't handle correction too well (same issue as seeking). There is no known list of problem media configs/types so nothing to avoid .. it either works or doesn't.
I'd be interested in a sample of the file for long-term testing with problem media, but currently there isn't anything I can do about fixing the decoder so my advice would be to transcode the file to H264.