Given what you're saying, you really need to find a cheap tone generator and hook it up to your amp and move the dial around and see what parts buzz.

If it's only one note that's causing it, the box might be ringing at that note, and you could probably fix that a few ways (change the box? Put a couple of bricks in it? Damp the heck out of the inside? Polyfill? One woofer?)