I solved the problem. Like how I caused the problem, I don't know what actually fixed it, but I went into the... myriad of config files, from the command line and from the configuration editor in EmulationStation, setting the shaders to "false" as per your suggestion and this fixed things, only the GB games were black and white instead of green and worse green. But I solved this in the quick menu>options>BG Colorization custom and >Internal Palette GBC - Green, although that second one may not be necessary.

The kicker is the game I've been playing, in monkeying around with stuff, I wound up making additional config files for this specific game, so it was still green(!) I used the File Manager in ES and went to /opt/retropie/configs/all/retroarch/config/Gambatte and deleted all the .cfg files except Gambatte.cfg, which was the file I had edited earlier to fix things (I think). But it works now and I'll leave these shaders and things alone for a while until I'm ready to make another big mess.