Sounds like you are bottoming out the sub. That happens when you over drive the speaker with too high of volume or too low frequencies. You either need to turn it down or possibly have to get an in-line subsonic filter that will block low frequencies that are below the subs low end rating.
You can get a CD with test tones or sweep tones that go down to 20Hz to see how low of frequencies your sub can handle.
You can get a CD with test tones or sweep tones that go down to 20Hz to see how low of frequencies your sub can handle.