Even at 40 times per second your eyes can discern a difference in their motion. If not, why do we have some people saying theirs run perfectly in tandem, while others dont? If our eyes couldn't discern anything at 40 cycles, we wouldnt be seeing different things from different setups.
The problem is, as someone else already said, most likely in the loading of the cones from the environment they are in (enclosure and vehicle). Certainly a port nearer one speaker than the other can cause uneven stress about their cones. Even having one sub mounted nearer an enclosure's interior wall than the other, or symmetrically about the single cone, can cause asymmetric cone motion.
In high powered applications like serious SPL setups, enclosure designers are careful to place the speaker symmectrically about the enclosure walls, and port, to keep stress on the cone even. Even in single sub setups.