Let's confirm a few things.

1. Are the two speakers in phase? I mean, is red or plus connected to red or plus on the other woofer?

2. Can you tell me some specs? It sounds like the woofers are being driven past their excursion limits. So can you describe woofer and box specs? Alternately, tell me Xmax, Vas, Frd and Qts for the woofers and also cabinet particulars.

3. Only one woofer pops? Does the symptom "follow the woofer", or does it "follow the position"? What I mean is this: swap positions of the two identical woofers, and tell me if the one that popped still does in the new position, or if the other woofer begins to pop instead.

4. What components are used between amplifier and speaker? Is there a crossover? If so, what kind? Is it a coil and a capacitor, or just a coil? Or is there more inside? And if there is a crossover are there separate connections for each woofer, or is there one connection that is shared by both woofers?

The answers to these questions will probably shed some light on this problem.