I had a similar problem with an Orion HCCA 12D - sounded almost like a scraping sound when you pushed the cone in. When playing it sounded like a wire was slapping the cone on the inside. Orions tech support said it was a warped voice coil. The sub still sounded great except when you were near the sub and could hear the noise...the leather seats covered it up nicely.
I believe it was caused from a leaky trunk and excess moisture on the driver...have any leaks in your car?