Well, if you're positive nothing is loose... than I'd take the route epistemology recommended. You could also try (depending on how you mounted the sub) positioning your box away from the back of the trunk (if that's where it's located). You may think it'll look 'off', but with a few 1.5" spacers (wood would be preferable), no one will be able to see the difference.
Hope that helps you in one manner or another. Good luck on getting it fixed!
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