I emailed Resonessence and they've come back to me already, which is great service. This is what their technical guy said:
The unit flashes RED briefly between sample rate changes on its input to indicate just that, It saw a sample rate change. What is happening with the OPPO is that between tracks, it is reverting back to some other sample rate (my guess is 48k) for a brief moment, before going back to the sample rate of the material. This is a bug in the OPPO in my opinion. What should happen is it should check to see if the next tract to be played matches the sample rate of the current track. If is does, do NOT change the SPDIF stream data rate between tracks. Based on the fact the OPPO can play a CD without changing the rates, proves its an issue with the OPPO itself.
I've asked if they can remove the fade in and play the music (albeit with more jitter) for the first second or so, as jitter is less of an issue than a missing drum beat (to me anyway). I'll let you know what they say.