One other thing that did catch my eye. Previously black, I think, was defined twice as something like 0,0,0 in Flash under normal and bright. When I changed from normal to bright back when you first played with colors I used them interchangeably and never noticed a difference. However, I see that all the systems that support bright actually defined bright black as a grey and that's probably worth emulating since you can always use normal black for black.
Allowing the user to choose between two color sets based upon weather they are using light or dark backgrounds isn't a terrible idea, but it might be hard to do. For instance I think I remember that bright yellow on white backgrounds was too hard to read for me so I couldn't use it, but choosing another yellow is probably tricky.
I think what you might want to do is something more like the following. Offer an option to replace the normal colors with the bright ones. As I understand that bug report you pointed at, the guy had the same problem I did. Namely the colors all became muted in the newer versions because his ANSI site was probably only sending normal intensity colors. I solved that problem by just adding a bright theme to all my servers, but he's stuck. He'd probably like an option to replace all the normal colors (but black!) with the high intensity color so he can get the brighter ones again like the older Flash v3.6 had. He liked the old version fine
