I would guess it's a bug in how the distro handles the common API for the color picker. There's a big change incoming that would avoid the problem in Pixel Proof. The next version has a built-in color picker that can grow with the needs of the rest of the program, launches faster, can be persistent, can pick transparency, can copy colors to the palette, etc. I'm not certain when I'll be able to release it, though, since I just started a new job and my schedule is very different now. Since you have an immediate need for it, I might try to wrap it up even if it is missing a couple of things.
Nah, don't worry. As I said, I'm not a professional game developer, I just bought this tool to mess with it so I don't have any hurry or immediate need. Since this is most likely a bug on the color API, I will file a bug on elementaryOS. Awesome to hear new features incoming though, but release them when you can and when you feel comfortable, no need to rush them.
Thanks for the fast reply!