Subwoofer Not Hitting All Notes

I just installed a new pioneer TS-W3001D4  1000 watt RMS and 3000watt peak subwoofer into my 06 explorer with the Audiophile system.  Its not hitting every note like it should, even when I had my old subwoofer in there it still didnt hit all the notes.  The Headunit is a Pioneer D3, and the amp is a Kenwood KAC-7251 (amp is only 460 rms).  I had this same setup minus the subwoofer ( i had a old pioneer installed) in my 06 F-150 and it hit every note just fine.  So I don't know what is going on with it.  Any help would be apperciated.

i am an idiot wrote: What notes is it not hitting on?   Upper bass,  lower bass?      What frequency is the crossover of the sub out on the D3 set to?     Is there a low pass crossover on the amp?   What frequency is it set to?

mostly on the lows, and some mids. i have the headunit's sub crossover set at 80 hertz and i have the amp's crossover set on low pass, with the input frequency set at around 80 hertz.

what enclosure is the sub in...sounds like a poor enclosure

I have no idea what you mean by "not hitting all the notes," but here's two thoughts.  First, use one crossover or the other.  If you want to use the HU low-pass, defeat the one on the amp (or set it to its highest setting.)  Second, is the amp staying on continuously or is it cutting out?  If it's cutting in and out, I bet your gain is way too high. Support the12volt.com

With the crossover set to 80 Hertz, I would expect no mid bass to come from the woofer. Try setting the crossover to 120 Hz. to see if it gives you some of what you say is missing.

My vote is improper tuning of the enclosure. Does it unload? What I mean is this: does it flap or move dramatically even down low, there's just no or very little output? That's improper tuning of the enclosure.It all reminds me of something that Molière once said to Guy de Maupassant at a café in Vienna: "That's nice. You should write it down."

Yes, if the enclosure is unloading the woofer it might sound like a wet fart instead of a "note."  Of course I hear systems every day that sound like wet farts so I assume this is desired by some users...Support the12volt.com

ok i think its the sub. i tried 3 different boxes, ad tried all different kinds of settings and it still deosent hit right. i put an old subwoofer of mine in to test it out and it worked awesome. so i'm gonna return this sub and get a JL 12 inch W3..hopefully the quality is better with that..