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PCSX2 always had problems with input lag, it's just the way it is with emulation in general. The fact that PCSX2 doesn't have real fullscreen just makes it worse.
The only thing you can do is apply general anti-lag measures, such as turn off v-sync. Other than that, you have to put up with it.
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We have been running tests due to the increasing number of reports and so far have found no correlation between exclusive fullscreen and input lag. The dev blog CK linked is a great read from Microsoft themselves about how, in simplest terms, exclusive fullscreen just does not matter anymore for input lag, or as a general concept, really.
Really all you can do is as Draconic suggested, experiment with vsync settings and see if that helps. Try both PCSX2's vsync options and those in your graphics driver. We are still exploring other possibilities (my personal, baseless theories are either MTGS desync or incorrect SIO2 interrupts), but our tests suggest PCSX2 input latency is matching or still somewhat close to the PS2 so we are still exploring this slowly and not jumping to conclusions.
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Could it have to do with the game you are running? Have you tested other games?
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I never had "severe" input lag back when I was running windows 7. Took a break eventually upgraded to 10 and noticed issues started occurring with PCSX2. Also, exclusive fullscreen still exists if you check the "Disable Fullscreen Optimizations" for the game you are running which can help with input lag for other games so I don't see why it couldn't here. PCSX2 used to have Exclusive Fullscreen did it not? Why was that changed? Plus we have this thread:
https://github.com/PCSX2/pcsx2/issues/3008
I understand you are "running tests" but if you are getting an increase in reports obviously something is up, also input lag DEFINITELY isn't matching PS2 hardware at all, or even that close as if played side-by-side I have definitely been able to tell there is a very noticeable more amount on the emulator. I can't even play FPS shooters anymore as it is just so hard to adjust to the amount of delay there is. Honestly I think this should be one of the top priorities since it is always being mentioned and can on certain games easily make them unplayable but I digress.
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Is it possible that somewhere over the last several years of PCSX2 development input lag started becoming a problem? Maybe it's related to a new feature that was implemented into PCSX2 at some point in time.
I would suggest anyone that is experiencing input lag to try going back to an old build from around 2015 and see if the input lag is still a problem on the older build. Maybe we can isolate when input lag started to become a problem.
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I am also noticing the Input Lag a lot, not it will be able to play FPS.
I have been playing mortal Kombat Armageddon on xbox and Dolphin and the difference is great does not present any Input Lag.
Specifications
RTX 2060 Super
Ryzen 5 3600
16 GB RAM 3000HZ
PCSX2 Vesion 1.4, 1.5 and 1.6
Pad: Xbox 360
Windows 10