Hello
Getting properly tuned boxes is a must but double check the high pass filter on the amp. What is the cut off rate it will listed something like 12db per octave or 18db, the higher the better. Is there an eq in the system that has everything in the sub low frequencies boosted to max? Also check and double check the system polarity/phase if one of the cabinets is backwards from the rest or even a speaker in the cabinet is reversed from the other that will significantly reduced your low end output make you want to drive the system harder to make up for it. If your system is connected with balanced cabling a simple mis wiring flip of + to - in a connector can cause the same thing. A peak stop limiter of any kind will only protect the system so far if the operator is determined to keep pushing into the limiter.
Mike Caldwell