Leave SHADERs and use OVERLAYs which simulates scanlines.

1 - install overlays from the retropie menu
2 - go to the folder:
/opt/retropie/emulators/retroarch/overlays/effects/scanlines/
take an overlay file and copy it to your computer, as well as your configuration file
3 - The overlay file is a png that can be cut into photoshop or other simpler programs. cut to fill exactly 640x480 in length.
4 - so remember in the configuration file and png file names etc where you have some resolution (example 1280x1024) you replace with 640x480

note that you are creating your 640x480 overlay from scratch

5 - enable overlays and select the one you created that has 640x480.

this is the method i found to make scanlines correctly match the pixels displayed on the screen

OBS: My english is bad, i am using google translator, i hope nothing written has got double meaning here too. Because in my post about EMULATIONSTATION LOCATION one person even complained.

Actually, thinking about this further, it might really be best to move the scanLineWeight * BLOOM_FACTOR out of the pow call. All this does is apply a nonlinear filter to the scanlines (why?), which should increase aliasing artifacts.

Another thought I had considered was using a quadratic Taylor series approximation to the gamma filter given by x^a ~= x*(1+(a-1)(x-1)), which works pretty well as in this quadratic approximation. A cubic approximation is even closer (but may not be necessary), as shown. But I note that someone seems to have had a similar idea here with these new "zfast" shaders, so perhaps those are already doing this sort of thing...

PlayStation outputs in both 240 and 480 lines. 480 lines don't look nice with filters unless you use a resolution that is a multiple of 240 (but not 720p because it's too low and will again be upscaled to 1080p by your monitor/TV).

You'll need a minimum native resolution of 880 lines (non-existent). The closet native resolution to a multiple of 240 on a commercial device is 4k (aka 2160p). This is impossible for gaming on a Pi.

I would recommend playing around with different shaders because I remember that some use tricks that simulate interlaced picture on 480 rendered lines, resulting in a shaky but more pleasing effect.

thanks dave for your help , love these shaders, i would not use the pi for emulation if it was not for those, they look super solid

Please ignore this - I found out what the problem was, I'd turned on Shader #0 Filter to LINEAR. That is what was causing this effect in lr-genesis-plus-gx.

I dont have a solution, sorry, for me its been the same since june.

Thank you!