I haven't figured it out yet myself.
Here's an example of how it happens:
Let's say I'm playing an FPS game.. MOA: Frontline, for example (about the only FPS I own.. hehe). While I'm running around, with footsteps and such, I can glance up at my reciever and see all the little "speakers" lit up (the ones that tell you what the system is using), with the window simply displaying "PLYSTN2" (which I programmed as the label for the Video2 input).
Now, if I'm in a quiet portion of the game with no ambient sound effects, if I stop moving, making no sound at all, those little "speakers" on the reciever will disappear.. the PS2 is outputting no audio signal whatsoever, and so the reciever "drops" it.
Then, if I suddenly fire my weapon, the "speakers" on the reciever will activate, and it'll scroll across "PCM 48KHZ" (or whatever). But, it happens a split-second too late, and all I hear out of the speakers is the sound of my rifle shot fading off into the distance.
Drives you nuts.
That's why I had to dig around through the manual and find a way to "lock" it into PCM mode permanently. So unless it's told differently by a digital signal, it'll decode PCM without having to figure it out first. So I no longer have the issue of missing sound.
I think the feature was added due to CDs, like you mention. That the reciever may "drop" the signal between songs, where it's recieving no signal at all, and then have to "recognize" the incoming signal at the beginning of the next song. This "PCM Lock" feature was no doubt added to alleviate that annoyance.
As I said, I just hope it's not a big issue with the next-gen consoles, since I'll no longer be able to use that feature.. I don't think I can "lock" it into Dolby Digital mode, it'll have to figure it out based on the incoming signal, which will be going through the same optical cable I'm using now. As long as the games are programmed in such a way that there's always some sound coming through, then it won't be a problem.