After sending in my subwoofer to JL Audio they tracked down the problem to a preamplifier component in the sub. I beat the odds and got two of them with the same exact issue in a row.
Sounds like they changed supplier or got a bad batch. These things do happen even with great products. Funnily enough though - the HT Shack Subwoofer tests reported another problem with the JL sub they received for testing - so this incident may not be as isolated as it seems - check the HT shack subwoofer test forums for details. I don't remember what it was - I seem to remember they observed significant audio compression below 40 Hz at high SPLs..