You have unequal loading on the subs. One sub is doing more work than the other around tuning because they're not loaded equally. Sounds like new box design time.
In this case, working harder just means one is meeting more resistance to cone excursion than the other, due to inconsistant pressure within the box at certain frequencies. They both still have the same amount of current flow through their coils (watts), so themrally neither is being worked harder so to speak. If either sub is possibly in danger, it would be the sub nearest the port that is unloading. It could cause premature mechanical failure due to over excursion, particularly when the signal deviates below the enclosure's tuning frequency.