My subs are not hitting evenly! Cause?

[rumdada 10+ year member]

Low bass is omnidirectional, as in the human ear is unable to discern its origin. But microphones can and do. Low bass is recorded in stereo, and the signal can vary from one channel to the other. If I was the OP, running multiple sub amps to different subs, I would definitely sum the sub signal to mono (via Y-adapters, or a pre-amp device).
If one sub was repaired, it likely will react differently than the old one. Different suspension compliance, if nothing else. With differences in impedance rise from this, it could alter performance fairly significantly from one driver to the other, depending on the box design. We also have no way to know who reconed it, or if it was returned to original specs. Having two subs that do not work (almost) identically means their output will not couple together well, making over all output erratic.

Im gonna call you Bill Nye The CarAudio Guy from now on! lol