I suppose that this is a bad time to mention that I ran well over 1500 watts into a pair or 12W0's and they held up fine.
Either way, it sounds as if somthing in your set-up was not quite right Tony. JL Audio woofers are about the least likely sub on the market to blow IMO, based on years of installing and competing.
Lets examine a few things, firstly- for anyone in doubt- a trio of W6's can be wired to 4 ohms mono. Take a look at this for how to do it:
Now that that is out there--->
What size enclosure were your W6's in? Also what type? Ported, Sealed, Bandpass-etc?
What were your gains set at on your amplifier?
I ask this, because what you said your subs did- is an exact symptom of an improperly set gain. If your subs behaved this way- they were clipping. Clipping results primarily from a gain control set to high or if one cranks the volume control most of the way up.
What frequency were your subs crossed over at?
I ask this due to the fact that you said one sub sounds scratchy now. That indicates to me- a damaged voice coil. Too high of a crossover point can lead to over-excursion.
What direction are the subs facing?
What type of music do you listen to?
What type of vehicle are these in?
One thing is certain, something is a miss if you are having these problems. Lets try and narrow it down a bit and get those subs moving for you.
In an old install I did, the guy was using 3 12w6's running off of an Earthquake PHD-2 amplifier, and they hit incredibly hard all together. So much in fact, that it hurt to be in the car. Your woofers are plenty capable, as with most JL Subs, they may just need a little fine tuning.
take it easy,
-zane