odd output issue

Alright, so I have had my same system in 2 prior vehicles with never having an issue. They were both Scion tC's so the wiring harness and such were the same. I now have a 2007 Charger that has a 6 disc charger with a factory amp. I bought a PAC C2R-CHY4 to retain use of the factory amp. I have everything wired up correctly, I have power to all speakers and my amp has power without fault. My system consists of 2 12" Alpine Type R subs in a custom ported box, a Hifonix 1200w mono class d amp, and a Pioneer AVH-P4100DVD HU. After hooking it all up, I had nothing coming from my subs. HU has sub woofer control on, remote line is connected, my subs are good after ohming them out and checking direct to a battery, all connections from amp to subs are good. Have each wired to 2 ohms. After tirelessly checking everything, I started to just adjust the amp settings to see if anything would happen after turning the level up. Nothing did. When I adjusted the LPF higher though, I got sound, but not very strong. Has anyone had this issue? I had my amp hooked up on a friends system temporarily last week just to make sure his system worked and it was fine as far as the LPF being set where I normally keep it.

try using different source......ipod to amp instead of deck, try front or rear rca to amp... could have bad rca, or blown sub out on deck,