Media encoder does not render audio when rendering video

Issue - A sequence that plays properly in Adobe Premiere Pro does not render properly in Media Encoder. It will not render audio when rendering video to H264 using any of the rendering methods or audio settings. It will, however, render the audio if the sequence is rendered to audio only, for example to MP3 or AAC audio.

Adobe Media Encoder version number - 25.0, however this has also been the case with previous Adobe Media Encoder versions since about last May. I had a separate bug report for previous versions but it was never repaired. I continued to use the older version. With the 25.0 upgrade to Premiere, and the lack of backwards support to previous Premiere versions of Premiere files, and this still being a problem, I was forced to figure out what the issue was with many trial and error attempts or completely re-edit my video.

Operating system - Windows 11 Pro. System is dual processor Intel Xeon Gold 6184 @ 2.4 GHz, 128 GB of RAM. Rendering is on a quad SSD drive. Video card is an NVidia Quadro RTX A4500 with 85 GB. available Driver 556.12. Does not matter if hardware or software rendering is used. I am listing all of this because here is no performance issue causing this problem, as has past no audio with video errors in Media Encoder or Premiere.

Steps to reproduce - Tracks are recorded with an Atomos Ninja. Audio comes in four tracks from HDMI recording from a camera - 1 through 4. 1 and 2 are blank on the tracks, 3 and 4 are left and right from the camera. Additional audio is on track 5,6,7 from a Zoom recorder. Mixdown works fine in Premiere. Typically rendering does not work in Premiere either for same version as media encoder, but have not checked. Does not matter if tracks 1 and 2 are muted or not. Video is ProRes RAW 4K 60 Hz. Recordings are typically 1.5 hours and the ProRes files are typically around 1 TB.

Expected result - Rendering a video from this file should produce audio along with the video based on the mix.

Actual result -  Does not render any audio when rendering video. Does not matter what settings are used in H264 for either audio or video. Renders audio fine when only audio is rendered.

Workaround - Split audio files so that track 1 and 2 that are bound to the video file are free to be deleted. Remove those tracks. Move existing tracks 3 and 4 to tracks 1 and 2 on the now split tracks so that the top audio track now contains data. Video will then render with audio.

I have tried all of the other reported fixes, including closed issue reports, going back to Media Encoder CC, as this problem has appeared in the past. None of them fixed this issue, including - cutting and pasting the sequence to a new premiere file. Muting and unmuting again, or soloing and unsoloing the mix track. Changing any rendering settings for audio in terms of sampling rate, AAC or AAC+ v1, v2, etc. Updating windows to the latest patches and rebooting system. Using a different setting for the rendering scratch files. Changing drives for the rendering.

Media encoder is also slow encoding files, doing about 31 passes on the audio prior to rendering video. I was able to render this without those initial passes typically, unless there was a time stretch in the audio, but that is no longer the case. I suspect the rearranging of the tracks in the way that I have done has caused this secondary issue requiring those passes on the audio prior to rendering video.