I've seen the same thing when I check the tracks that i produce. During mastering in order to check the sound also on my amplifier I create a wav file, copy it on a USB stick and then put it in the CDJ (the computer for production is another room so I cannot connect it directly to the amplifier). I do not want to waste time in rekordbox, it's just a temporary version of the mastering that I might need to adjust again (equalize, compress...) after listening to it, so i do not analyze it.
The bpm of the tracks is obviously 100% steady, it's electronic music generated by Ableton, but when I put it in the CDJ the bpm readout would fluctuate continuously exactly as Walter describes.
The actual bpm of the track does not drift, it's stable, and you can check it by beatmatching by ear with another track analyzed in rekordbox or coming from traktor. It's only the measurement, the bpm readout on the display of the cdj that fluctuates a bit. Apparently the CDJ 2000 nexus is not able to provide a 100% precise bpm readout as it analyzes the track in real time while it's playing.
Analyzing the track with rekordbox you will see a steady bpm on the cdj. That's exactly what happens to my tracks after I'm done mastering: i create an mp3 and then analyze it with rekordbox. After analyzing the track the bpm is not fluctuating anymore. It's only the real time bpm measurement that does not work.
Basically we have a 2000 € device that doesn't analyze the bpm much better than a 200 € cheap mixer with bpm counter.