AFAIK, there is no compatibility issue between V16B1 and SH3 Commander. Many people on this forum use both successfully.
It sounds like you may have SH3 Commander set up to overwrite menu_en.txt. Uninstall Commander completely and reinstall it. Do not make any changes to Commander (except to add the .cfg file changes if you are using GWX or NYGM). That should get you to a clean baseline and eliminate the problem.
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