These cars are very sensitive to voltage fluctuations. What is the amp grounded to? is it bare metal or a painted surface? Also, depending on how strong of an amp you're running (and how high you have the gains set to), when the bass hits you could be having some serious voltage drain for that momentary boom. How old is your battery? If the system is big enough, maybe running a capacitor in line between the battery and the amp would be a good idea.
I run a 10" Pioneer with a 2-channel Jensen bridged (I do not recall how strong), but I wasn't going for any big boomy bass, just more low fill that the Bose can't hit. With a fresh strong 850CCA H9 battery, and no capacitor I have no issues (3yrs with it now). I do have the amp grounded at the battery hold down bracket between the bracket and the bolt so it's a bare-metal ground point.
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