There are two things I would do:1. Take one of the subs outdoors and measure it. That will tell you what the anechoic response is, and let you know if the problem is in the speaker or in the room.
2. Model the room with CARA to find out where to put your subs for smoothest response. Using careful placement, you can average the room modes, effectively cancelling notches and peaks. For example, where a notch would form from a standing wave cancellation when just one sub is used, the other sub can be positioned so that it fills in the hole. When combined with the woofers in your mains, you'll have four bass sound sources to blend, further smoothing the room modes.