Hi James,
Not that i have any experience of the audio system you have there, but a couple of questions..
are the sets of music files (ripped and amazon) on the same usb drive ?
might be a number of causes..
the format of the usb stick is incompatible most things can read fat (google fat filesystem for some background info), so perhaps the device you have the amazon files on is incompatible, or can you see the filenames but not play them when selected?
the other more likely cause is either the bitrate of the .mp3 files, if you try looking at the 'properties' of the working and incompatible files you might discover the difference.. bitrates go up to 320kbits on mp3 files, also have a look in whatever program you use to rip the cds to see what format or settings are being used, some background info here..
https://en.m.wikipedia.org/wiki/MP3