The most common reason for the symptoms you have described is a narrow room mode that only certain songs excite. You can have up to 20 dB or more in one very narrow band. EQ is usually the best way to solve this particular issue. This implies measurements though, but the problem should just be glaringly obvious once you measure.
Sometimes there is a related issue, where 1-2 peaks cause the listeners to set the overall subwoofer level too low. Once you clip the peaks you can then raise the subwoofer to taste.
Of course, bass traps and subwoofer placement also are useful but if the problem is as described, an EQ in just the sub can be magic.