I have the Apollo and don't have this problem. However, I treat my Cds more like LPs and they don't have any scratches to speak of.
Rega makes a big deal of the fact that the Apollo and Saturn analyze the CD before playing and optimize the player for each CD. It's possible that this means backing off of some of the error correction logic if able and that the player is being fooled in this particular case. This might also account for the sensitivity to vibration that Electroid mentions (although I have not experienced this). If the player were to back off of most of its error correction believing it was not necessary for a particular CD and was then hit with a large vibrational peak. Again, this is all speculation since, as far as I know, Rega has not provided details of this "optimization" routine.