I use digital (coax) connections from my Pioneer DV578A and like you, MWR0707, I complained here and learned the same thing. Now I live with it as a moderate nuisance, though I agree it would be nice if the processor could simply start in CD mode. Unfortunately, as Gonk told me, if the disc signal is in some other mode there could be a burst of noise that would be a lot worse than silence. Some tracks, on the classical music I usually play, begin with a couple of seconds of silence, which is long enough for the 990 to lock on to the signal.
But wouldn't it be possible to make a remote macro procedure that would respond to the "play" command by (1) mute, (2) play disc, (3) wait 2 or 3 seconds, (4) stop, (5) unmute, (6) restart track 1? Of course if the user intended to play some other track the macro would have to store that track signal first and then repeat it as the last step.
Does anybody know of a remote that has this capability, including storing the desired track?