One thing that I observed while playing with my board is that when I use the default skin thats included in the software dl, that not only does the volume graph change, so does the other three but on a smaller scale...I have looked at the skin and don't see any reason why input on one port should affect any of the other readings...??
And BTW which is port 0 for the AI, is it as marked on the board?? If so it would make it much easier to have them in order starting at one end.
On the idea of a retro fix addon, I was thinking of actually making a daughter board that this would plug into so that I could change the pin headers into a mix of either headers or wire terminals, to make highly universal... I don't think that will be to difficult.
Another observation that I noticed was that just playing around with it only driving the output LED's that the v-reg got pretty hot as seeing that its shouldn't be comsumming alot of power between the uP and leds, little alone driving say 3 or more relays. I might, just to be on the safe side, remove it and add a small heatsink that I know I have laying around...maybe a change for v2.