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.