I experienced the same issue with a purchased iTunes song. I tried deleting the song from the Clip Zip several times and retransferring. The song messed up in the same exact position every time. I have not tried changing the USB mode.
In contrast, this same song plays perfectly on my computer and smartphone.
I fixed it by transcoding it into MP3 320kbps. I know, that’s not solving the root cause, but it made the song play correctly.