It could be how windows is handling the handshaking with the tv. I know sometimes windows can take longer with tvs. Try another emu to see if maybe the emu is bugging out because of this. Or even turn on bezels as windowed mode most likely won't have this issue. HS is also sensitive with focus as I never heard the focus bug was ever truly fixed.
Also is the emu simply in the background, or minimized?
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