Sounds to me like your subs are out of phase. If you were to take your box apart and switch the wires on one of your subs, the problem should be solved. When the two speakers are out of phase 180º they will nullify each other to some extent. You will notice much better bass response if they are in phase.
You got the fix for the wiring, now seal the box. If you want the most sound possible, take the speakers back out of the box and run some liquid nails, or silicon around the inside seams of the box. I guarantee this will make the sound a lot tighter. I've done this with every box I have ever had, and I can't tell you how much better it makes the subs sound.
problem with silicone sealant is that it's soft. it seals, but doesn't make the seal hard, it always remains soft. you want a hard seal. when you rap your knuckles on the sub box you want a tight high pitched "clink", not a dull low-pitched "thunk". the more rigid the box and seams, the tighter the bass. use gorilla glue, it dries hard. also consider internally bracing the box with scrap pieces of wood. that also helps increase the rigidity of most boxes. in fact, the effect of structually reinforcing a weak sub box can be like night and day. remember that it's the resonance of the box that produces most of the sound. without a structurally tight box, even the best subs will sound loose.
am sorry to say this but is your box one chamber or two, if its one chamber your subs share the same airspace which means your subs will work against each other ( one pulls in and one push out ) a two chamber box is when each sub has its own airspace , so your subs will work together ( both work in sync) with each other
easiest way to look at phase on a speaker is to simplify it
your subs (or any speaker for that matter) need 2 sources of power + and -
from memory i think the + signal is the one that pushes a speaker and the - pulls it (without getting technical)
now if you have a + wire on a - terminal on the speaker your speaker will in fact pull instead of push as it's getting a signal to the - side of the speaker (pulling side)
to get these to work in unison you need to make sure that the two + wires from your amp are infact going to the + terminals on your speakers so that they will both push at the same time
hope that's not too confusing for you
if you need more clarification PM me and i'll be glad to help