One thing I would do would be to go back to your JL dealer and have their techs look at them. Are the speakers getting to much bass for them to handle? If so bass blockers work nice. Do you have them wired correctly, are the wires reversed. In any of the possibilities, I would take off the speaker cover and go to your dealer so they can give you their professional opinion.
Well, they should be wired correctly, they have certain size connectors for certain connections so, its pretty simple, I'm running on the factory deck, so I don't think I'm pushing too much bass to them. I bought them brand new on Ebay and the warrantee has gone out so, I don't have much choice but to replace them, cuz a repair will probably be too expensive.
if it's popping--obviously too late...but generally--it means that they we taking on more bass than they should have....
inspect the speaker...push the main driver down in a perfect vertical motion--or even slightly off center...if there is a wiered scraping noise...thay're crapped....