Q Logic Custom Enclosure

It's hard to really figure this out without listening to this hollow sound. If the amp is installed and set up properly, and the speaker is in perfect condition and wired correctly it could be the enclosure, a combination of the enclosure/sub, or the combination of enclosure/sub/and vehicles acoustic dynamics, or lack thereof. with only one sub it shouldn't be a phasing problem per say, but can't hurt to reverse the speaker wires to the sub and see if you notice an improvment.

I find Q logic products to be pretty good usually as well as infinity but I know if I was building the enclosure for that vehicle it wouldn't leave my bay until it sounded great.

Might want to try a different setup, either MDF or MDF/glass.

Have you tried it without the polyfill???  I had a sub that did that (Phoenix Gold Xenon 10D2).  I had it in the box fill with polyfill and it sounded hollow, however...removing the polyfill cured the problem.  If my understanding is correct, you only want to use polyfill in a case where the volume on the box is smaller than what the specs on the sub call for.  The polyfill makes the sub think it's in a bigger box  (not quite sure how that happens, but that's the explanation).

Also, what is your LPF cutoff set at?