So I remembered that I needed to share this with the world. It confused me on a few shows before I talked to Bruce and got it figured out.
So in the menu for the Puck Q12+ and Fab5 at least (I'm sure any others that share the architecture) there is a manual setting for the colors. At times trying to go through and set a color to use without DMX control I've tried to use that and through somewhat random button pushing sometimes it worked and sometimes it didn't. What this actually does is provide a final override step right before the actual LEDs. It essentially is a dimmer for each of the colors individually that effects all of the sound active, automatic, preset color and DMX modes.
The important thing about that is the DMX. All the other automatic, sound, etc modes get over-ridden when you plug in a valid DMX signal but this one still effects it. So what happened for me was that a couple of my lights couldn't show green. Everything else worked, addressed the same, passing signal fine, if I do a test on the fixture the greens work. Turns out someone has set the manual for green to 0 so it was changing the DMX sent value down.
So in short, at least be aware of those settings and either avoid them or disable when needed. Now understanding how it works I may use it some to dim my Q12+s down a bit. They are ridiculously powerful for some of the stages we do and can overtake some of the effects.