Griff, you are extremely unclear in your writing. to be of any assistance, some facts need to be established.
You know, it's highly possible that JBL sub is toast. Let's explore that possibility. Answer these questions.
First off, Where is that Bose equalizer connected during all this? They add an ungodly amount of bass boost so it's possible it could overdrive the woofer. Take it out of the circuit for these tests.
First, disconnect both subs from the receiver.
Now, hook them up, one at a time to the receiver. Remember, disconnect the first sub when connecting the second one.
Do they both work? Do they both make that noise, or does only one make it?
If only one makes that noise, which one is it?
Now, if NEITHER made that noise, connect them both up in parallel.
If one again makes that noise, which one is it?
If the noise hasn't occured yet, reconnectthe Bose equalizer and tell us what happens.