I had a problem like that and I had no idea what was wrong. I ended up closing the codeplug and starting over. That fixed it IIRC.
that's what I ended up doing too, luckily this was a modification to an existing codeplug, not writing one from scratch.
I tried to replicate the problem, and it seemed to appear when I deleted an un-used MDC system, however every personality, and every MDC Call, had the other MDC system selected, I couldnt find any other place for it to be selected, and of course the CPS was no help, just gave me that error when I clicked on it.
I guess it wont be harmful to leave the other MDC system there, it was in the radios when I first read them from whoever wrote the codeplug before me, and it shall live on