Setting Up Indexed Gradient Ramps (no intermediate colors allowed)SUP
What version you running?
I'm on CC 2014.1 (current version), so it might be different for me, but to solve the issue you're having all I have to do is click where the stops are. Careful not to drag at all. JUST one click.
When I click two stops stacked up in the same exact location, Photoshop will toggle between which one is getting selected to allow me to see it and drag, but at the same it actually changes the overall gradient.
Where there are two stops stacked on each other, it looks like only one is there. So, if there's a red and a green one stacked up, when you I click that red stop, it looks like it turns green, but it's just the green stop being brought to the top of the stack.
The last few versions of Photoshop implemented a number of little ui tweaks and workflow smoothing gimmicks so the toggling click I can do might be a recent thing. I don't know.
But if so, that's ok. There's another way I found.
When stacking up stops, you want them to affect the overall gradient ramp in a certain order. I found that you can alter stacked stop ordering if you drag one stop out of the stack and then just put it back. Just keep doing that until PS gets it right.
Let me know if this still doesn't work. I wanna know.
Some 1-bit anims, using this method, would be awesome. Just like your avatar.