Photon do you have VRR screen? With Freesync I sometimes get these problems too. Perhaps it's related to how DWM handles windows on VRR screens?
You might like to see if switching Variable Refresh Rate option in Windows' Graphics settings changes anything...
Also see if WinUAE has any profiles in nVidia settings - I had some funky stuff going on when I had some sync-related settings set in WinUAE Radeon profile.
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