yes i use analog connections on my CD player.

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?

The Philips Pronto can do that. You could create as many macros as you want and they can include delays. The Pronto is completely customizable. I may have to play around with that.

I am prety sure you could do this with the Harmony remote also. Jim

Any remote with macro capabilities could do this (Harmony, Universal MX's, Pronto, ...).

Thanks for the suggestion regarding a dedicated CD player with analog connection. That sounds like the best option so far.

mwr0707,
another good reason for using a CD player for your CD listening.. they sound better in most cases than a DVD player will.

I know there is debate about this.. but especially in the DVD player that are sold for under say like $250 category.. a dedicated CD player will usually beat it soundwise.

I use a dedicated CD player also, an older Sony 5 disc carousel, Sony CDP-545, that sounds great and no lag but I do have it connected via optical.

Interesting, I wonder if the decoding process is different for a digital input associated with the CD source?

The signal acquisition has to operate the same way because there's no way to know what signal might crop up. The 990's acquisition is generally pretty speedy, though, and so on some discs (those with a little "dead space" at the start of the first track) it's effectively impossible to identify the lag. There may be some dedicated CD players that start a PCM signal before starting the disc, I suppose, but I don't think either of the ones I've used via digital output did.