Media Encoder creating unusable repeatable lagging video from MP4 video

I am seeing a new issue where only .mp4 video encoded produces repeatable lagging output (like duplicate frames, not a player issue) where other formats used in the composition have no issues. This issue did not exist in the previous version of ME. Software and hardware renders produce the same results. The MP4's converted to sequential images produce proper results. The MP4's (that worked before) files are all local. Rendering out of Premiere Pro produces the same results so I don't know where this lives exactly. Recent renders of this edit  with the same video files do not have the issue.