First thing I would do is bring in two known good, matching speakers and hook them up in place of the speakers you're having issues with to make sure you don't have an issue with your amp.
If that's all good then you could have an issue with one of your drivers; shorted voice coil or some such. One of your subs should not move WAYYYYYY more than the other, regardless (that sounds like a woofer is out of control). Disconnect the R speaker completely (make sure you don't short the speaker leads) and make sure the L, when fully connected, sounds like it's supposed to. If that checks out, then disconnect the L and hook up the right. Sound like it's supposed to? If so then hook them both up. If suddenly the sound goes to **** I'd say you've got a speaker out of phase somewhere... if it sounds like it's supposed to then I've fixed your problem magically across many miles, and you owe me $50.00. I accept Paypal, cash, and chickens.
Peace
LO