I've had a similar problem today with the sprite of a shadow.
I wanted it to be more blue and transparent so my code was:
shadow.AlphaColor = MakeRGBA(13, 5, 54, 100);
But nothing happened.
After checking the sprite in SpriteEdit, I saw the opacity was already set on 100.
So WME was reading only the setting from SpriteEdit: (255, 255, 255, 100).
After setting the opacity on 255 in SpriteEdit, the code in the script:
shadow.AlphaColor = MakeRGBA(13, 5, 54, 100);
started to work normally.
So if your buttons are sprites, check on SpriteEdit if, on every frame, alpha color is set on (255, 255, 255) and opacity on 255.
Then maybe your code in the script will work as expected.
Hope this helps!