When you say several systems now all show the same shader are those systems all using the same core, ie gameboy, gameboy color, gameboy advance? If so it sounds like when you applied the shader you saved it as a "core override" applying it to all systems that use that core (or you may of even saved a "global override" meaning its now used for everything. You need to load a game that uses the shader, go into quick menu/shaders and click on the button that is a "remove override" it will be named differently depending on what sort of override it was.
In future you should be using "content directory overrides" for things like this, Sega is a good example of this, the genesisgxplus core emulates sg-1000, master system, megadrive, mega cd, pico, and game gear, you wouldnt want the same settings for all those systems, especially game gear and the home consoles, so you save a "content directory" override. This saves those settings for any game loaded from the same folder as the current game, so if you had a game gear game loaded in future any game loaded from that same game gear rom folder will get the same settings, but something from the megadrive folder wouldnt.