If you were using the line-in (as opposed to the optical-in) on the JB3, it's possible you set the format to be WAV, but used something other than 44.1kHz (e.g., 22.05kHz, 11.025kHz) as the sample rate, which would still give you a WAV file, but one that's a lot smaller (like half or a quarter of what it should be).
I did this once, when I had forgotten that, when using optical-in, there's just "WAV" format (no sample rate), but when using line-in, you have to select WAV and the sample rate. One night I recorded optical-in, followed by a line-in recording the next day, and ended up using 11.025kHz sample rate on it, as it was the format that's in the place on the menu where "WAV" is for optical-in recordings.
Aloha,
Brad