I thought Mark Hennessy explained it pretty well.
A speaker's enclosure and crossover network are designed and built for a specific combination of drivers. The volume, shape, tuning frequency, crossover frequency, slope, etc. are all based entirely on the drivers' Thiele/Small parameters (T/S for short) and frequency response. Speaker designers make sure that when they design the system, they use the T/S parameters for fully broken-in drivers, since that's how the speaker will spend the majority of its life. This of course means that before the drivers are broken in, and the T/S parameters are out of spec, the enclosure, crossover network, and drivers are all mis-matched. This can result in unnatural resonances and lulls in the response, a quicker-than-normal rolloff on the bottom end, some quirky behavior around the crossover frequency, etc.
Edit: too slow.