I can get rid of 90% of the problem by setting the ALC V filter all the way down to 1. There’s still a little bit left at the part closest to the game image on the bottom. Its a flickery line that goes from the center of the screen to the right and its the first row right under the game window, it looks to be 1 pixel tall. I don’t notice any flicker in the game itself thankfully!
Thank you so much for the help! 🙂 Do you have any inkling as to what may have caused the black level to be increased? Could it be indicative of some kind of problem? For what’s its worth, the issue appears as a red noise on my PS2, and was also red on my SNES to begin with, but after I redid my RGB bypass it changed from red to the white I posted in those pictures.