At first it sounded to me like a jitter problem. Your DAC isn't correcting for it, so that's going to be the only difference between a cdp out and your mbox out, all other things equal.
Now, when you say that there is a difference through the mbox between music from the hard drive and a cd in the tray of the same computer then that points to a setting in itunes that somehow doesn't affect direct playback (which I didn't think existed). In the audio tab in iTunes Preferences do you have "Sound Enhancer" or "Sound Check" turned on? In the importing tab are you selecting "Use error correction"? Beyond that, the most important settings are going to be for the mbox.
Perhaps you should run Norton Utilities on your hard drive to see if there are any physical problems? I've done this test with a number of computers, several audio interfaces, multiple DAC's, and in studio and living room scenarios. They've always sounded equal to my ears (and barring any physical defects in your equipment) they should be. Technically, there are well-defined validity checks built in to hard drives so that things like this don't happen.
Now, when you say that there is a difference through the mbox between music from the hard drive and a cd in the tray of the same computer then that points to a setting in itunes that somehow doesn't affect direct playback (which I didn't think existed). In the audio tab in iTunes Preferences do you have "Sound Enhancer" or "Sound Check" turned on? In the importing tab are you selecting "Use error correction"? Beyond that, the most important settings are going to be for the mbox.
Perhaps you should run Norton Utilities on your hard drive to see if there are any physical problems? I've done this test with a number of computers, several audio interfaces, multiple DAC's, and in studio and living room scenarios. They've always sounded equal to my ears (and barring any physical defects in your equipment) they should be. Technically, there are well-defined validity checks built in to hard drives so that things like this don't happen.