No, I was using the ADI2 FS Pro in preamp mode -- analog line level in, headphone out.
Unless I am mistaken, both the JDS Lab Atom Amp 2 and the RME ADI Pro FS have only one analogue input.
That means that it is not possible to make comparison between two sources through their respective analogue outputs, because you have to stop the CD, unload it from the CD player tray, close the tray, switch the Atom or the RME and the CD player off, unplug the modulation cables from the CD player, plug them to other other player, switch the Atom or the RME and the other player on, load the CD you just listened to with the first player in the second one, and then only listen to the new player.
The delay introduced by this procedure is way too long to make any meaningful comparison.
Furthermore, you wrote you make sure to level the volume by reading the dB scale displayed on the RME. But this display is not an absolute measurement of the RME output level. It is just a reminder of the setting of the volume control. If the two CD players have not exactly the same output level, the RME output level will also be different if the volume level is left unchanged, because in that case the RME apply the same exact gain to two already different input signal levels. Needless to say, it is simply impossible to ensure that both CD players were listened to at matched levels with the Atom, unless a measurement with a test tone on a test CD has been done to check that the volume knob is set such as the Atom output level is kept the same before proceeding to the listening, which would lengthen even more the delay between the listening sessions of each CD player.
In order to make a meaningful comparison, you should, at least, procure yourself a preamplifier that have two identical analogue inputs
and the ability to trim the level on this inputs, or to memorize an offset of the volume control when switching from one input to the other. Any one of this features will be used to compensate the difference in output levels of any sources to be compared when playing simultaneously two items of the exact same CD release.