Hmmm, glad checked back in on this thread. I had let it slip from my mind (all too easy these days). I have not experienced most of the problems noted above but I do tend to mostly listen to entire discs. I have not yet had a disc that refused to stop playing. However, I have occasionally had initialization problems and, now that you mention it, I've had problems skipping to the correct track (from the remote). This happened just yesterday. My recollection is that this mostly happened with CD-Rs and I had just chalked it up to the vagaries of cheap media, etc. although I am careful with my burns and always use 8x (my CD-RW won't burn any slower).
Doug is correct, you definitely learn quickly to leave the player alone until the "Initialising" (for our UK friends) finishes. Steve's information on unplugging the player is interesting. As someone who works with computers, it is feasible that, since there may be current running through the player even when switched "off", it might accumulate and eventually be confused by those premature commands. Since I unplug my equipment when thunderstorms come through, I may have inadvertently avoided some of the problems. I do think they need to be fixed if there are problems. I also wonder what that fix would entail. I'm not sure that the firmware is flashable and the chip is probably soldered to the board although I confess that I don't know for sure on either of these issues.
I will say that my Apollo is one FINE-sounding CD player. Although I have not had dozens of players in my system, I never really understood what PRAT was until I found my foot tapping with the music while listening to it.
I hope we haven't scared Steve away from this thread as he would no doubt provide valuable insight, and possibly a conduit for communication, with Rega.
Dick