I know that this message is extremely late, but I had the exact same problem that only affected Skyrim when launched from MO2, I was going to do what the OP had done but I instead did the following and this has worked for me so I am going to leave it here:
Open the SkyrimSELauncher (Not SkyrimSE either by going to your steamapps folder or by browsing the local files of SkryimSE from steam) > Select Options > Disable both Borderless and Window mode:
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Hopefully this helps someone later down the line. Good luck!
