My two cars were the same way. My 94 had JBL, my wife's 95 had premium, and the same thing happened. Without a sub, I couldn't tell if there was a bass track or not, while my wife's car shook the crap out of the car.
One day, for gits 'n shiggles, I swapped the two amps. Voila! My car shook like crap! And my wife's didn't!
Basically, the JBL has a low-band crossover that it sends to the sub amp instead of the speakers, so the corner speakers don't get all that boomy bass that they're not good at handling (besides pounding the car, it sounded like absolute *****).
So, with the sub, the bass level is still a little less, but it is light-years clearer than the Premium sound produces. That's the JBL difference.