No - it's not. The problem is clearer now.
The CDs you are playing are being converted from their full bitrate, which I believe is about 1411kb/s, you're comparing that with mp3 which can be encoded from 128kb/s and up. They will sound different, and should. As you increase compression, you'll lose details, reduce the dynamic range, etc.
There are a few possible solutions, but given the high quality of the equipment you are playing through, I would recommend that you either accept that it will reveal these differences, or else work to eliminate them.
1. Ensure that you have at least 320kb/s set as your compression rate when transferring CDs to iTunes. Preferably use lossless encoding - this will give you smaller files that contain all the information on your CDs.
2. Consider using a stand-alone DAC between your AE and the BS9000. The DAC can convert the optical Toslink output from the AE to an analog signal that you feed to the AUX on your BS9000.
The sound cards in both the Mac and the AE are not very good, and do not convert to audiophile standard.
Make sure that you have Equalizer and all sound enhancers switched off in your Mac/iTunes -- if you have any EQ effects set you'll degrade the signal further.