It would be unusual to have the low bass be correct with 1 of 2 subs out of phase. It sounds like these are passive subs? If so, be sure the amplifier connections are correct/matching. If using Speakon connections or something similar, use a meter to be sure they are wired correctly.
They may also be overlapping too much with your full range speakers and sound "better" (less bloated?) when the subs are cancelling one another.