The Submitter is a MAXScript. So it is quite easy to test if it does anything wrong.
When SMTD is saving the scene for submission, it is actually using the Hold/Fetch mechanism of 3ds Max.
This has historic reasons (older versions of 3ds Max like 5.0 and 6.0 did not have a flag to save the scene without changing its file name), but it also tends to save faster than a regular File>Save operation.
To test whether SMTD is actually corrupting the scene when saving, simply load the original scene and execute in the MAXScript Listener:
holdMaxFile()
fetchMaxFile quiet:true
Most of the time, the Submitter only executes the first line, then sends the resulting file to the Repository. It only performs the fetchMaxFile() if the scene had to be modified before submission (for example if Merge XRefs On Submission was requested).
If your scene is in good shape after running the above code, I would say there would be no reason to believe that SMTD has anything to do with the corruption (esp. since it is using MAXScript functions written by Autodesk to save the scene anyway ).
If the scene IS corrupted after the fetchMaxFile() call, then it would explain what you are seeing, but it would still be an Autodesk bug.
Please let us know the outcome!
If it does corrupt the scene, we could experimentally replace that saving code with a saveMaxFile() call and see if it changes anything for you.