In the past we've noticed that there are sometimes issues importing MP3 files that occur when the program converts them to WAV for use in the Audio Chord Wizard.
It's probably not this, but since the comment was made that some MP3's don't work (but others obviously do), it makes me wonder if it's something like the difference between VBR (Variable Bit Rate) versus CBR (Constant Bit Rate) encoding, or maybe a result of the CODEC (Fraunhofer, LAME, MP3Pro, etc) used to create the MP3 in the first place. And of course, is the DEC part of the CODEC on your machine up to the task of decoding the MP3 file?
I would experiment with a variety of files to see what the problem might be.
Just a thought.