Oh, sorry. I suppose I read your question incorrectly the first time. I place the .shader files in the folder titled "shaders" within the .pk3s.
@@eezstreet
I'm not sure why, but your suggestion worked. The game must have been determined to use the original gfx.shader file over the new one that I created, because as a result, overwriting the old gfx.shader worked. Do you have any idea why the new .shader files I was making could not overwrite the old one?
Vegeta's post in Realistic Water Splash was marked as the answer