Possibilities:
1. When a signal arrives at the digital input, the receiver tries to identify the type of signal to determine which decoder to use. When you play the first track, it has identified the signal as PCM and plays it accordingly. It sounds like the time it takes for your cd player to skip to the next track is long enough that the receiver senses there is no signal and reverts back to its default decoder for that input. When it starts playing again, it takes it a second to identify the signal again and realize it is still PCM.
2. You have both analog and digital connections to the cd input and the format is set to 'auto'. Again when there is a pause, it polls the inputs to see which has a signal - analog or digital. It checks the analog input to find no signal just as the data from the cd player arrives, then checks the digital input and sees a signal there and tries to identify its type as in #1.
You could temporarily try setting the input format to 'digital' or 'pcm' (whatever your receiver's setting is) to eliminate the polling of the inputs. If that works, then the receiver is just a bit too slow to identify the input and determine the signal type.
3. The cd player itself is slow to skip to the next track and start sending the data to the receiver, which naturally causes either 1 or 2 to occur. As an experiment, try a different cd player.
If it is 1 or 2 there really isn't much you can do about it, other than manually set the format to pcm for that input so it doesn't auto-detect anything.