Front loading the subs with your plexiglass idea wont solve the problem, merely mask it, and not by much at that. After seeing the enclosure, Im thinking the problem is most likely what I alluded to earlier, non-symmetrical port to sub location. If one sub is closer to the port than the other, this can and most times will alter cone motion when comparing the two drivers. Contrary to popular belief, pressure inside the enclosure is not uniform. Ideally in a shared chamber multi-sub ported setup, all subs will be equidistant to the port, so that each speaker will exhibit the same pressure variations at the same time. If one sub is closer to the port mouth than the other, pressure will not be the same between both drivers, and visible cone excursion difference can become present. This phenomenon is not always visible, but if the subs are not symmetrical about the port, its always present. Variances in subwoofer suspension compliance due to differences in break-in periods would only serve to increase this excursion variance.