Check the polarity of your subs. Make sure that they are connected properly. If you are using a 2 channel amp with each sub connected to it's own channel try flip flopping the polarity opposite of the other sub. I have had that same problem in the past and that took care of my problem immediately.
if for some reason you have negative to the black terminal and positive to the red terminal (normal) on both and they are misfiring switch one of them around so that one is normal and the other is negative to the red and positive to the black. I had the same problem.
i noticed that on mine. there's air coming out of the side of the box on the left side. but it appears that the left sub moves correctly, as if the right sub appears to be off beat.
on mine, when they were missfiring it sounded like... god knows what in the trunk (and it wasnt loud or bassy at all). The difference is night and day times 10