turn on thump with new head unit

My system consists of a Pioneer CD head unit, aftermarket speakers, and an MTX 2-channel amp (older) powered an old JL 10W0 subwoofer. Today I replaced my older Pioneer CD head unit with a newer Pioneer head unit, and now when the amp turns on or off, the subwoofer makes a "thump" sound. It also does it when switching between the tuner, CD, and Aux sources. I did not get this thump with the old head unit. Also, the old head unit only had 2 pairs of pre-outs, so I had my RCA cables on the rear pre-outs for the sub amp. The new head unit has 3 pairs, so I have them on the sub pre-out. Could this make a difference? I did use the same harness I using with the old head unit. The wires on the Pioneer head unit plug are all in the same place as the harness that came with the head unit. The remote turn-on wire is connected to the power antenna wire on the vehicle's radio harness, and then my amp turn-on wire is spliced into that antenna wire. I no longer have a powered antenna on my car, so I'm wondering if I should take that turn-on wire from the stereo harness and connect it straight to the amp's turn-on wire, and not have it connected to the car's power antenna wire. Any ideas on this one?

well, this morning I found the battery drained on my car. Seems like the amp was on all the time or something. Maybe this is the reason for the thump sound, because the amp was already on? I haven't had a chance yet to investigate the wiring to see why this would have happened.

More info: When I plug the harness into the back of the head unit, everything is normal. When I turn the car on, the amp comes on like it should. However, when I turn off the car, the amplifier stays on. It stays on until I unplug the harness from the rear of the head unit. This didn't happen with the old Pioneer unit. Could I have received a defective unit?

patrick, i have the same problem except my amp turns off, the thumping sound happens when i turn my deck on/off,switch between tuner/aux/cd, and what not, id say ur best bet would be to make sure ur wiring is all right, my p6500 is terrible with the thumping so i just installed a switch inline with my remote wire sounds like ur remote or ignition one isnt wired right, i had that prob with my old alpine and it was the fused ignition wire was lose, what deck is it?

It's a DEH-P4900IB. I tried both my old harness, and the new one that came with the head unit + the adapter harness for my car. Everything was wired the same, and I checked the wire connections on the car side of the radio harness and everything matches up.

id put my money on that its ur deck, im 98% positive its mine, but really im not qualified to say anything, but id goto where u bought and and see if they can test the deck/switch it and see if it really is the deck

Bought it from Crutchfield. I might have to use their 30-day return policy, but it sucks because I already installed my old deck into my wife's car. I spoke with a tech guy at Pioneer, and he basically acted like an @$$hole to me, but said I needed to verify that the turn-on lead is in fact sending 12 volts after the car is turned off. I guess I should have done that already but I'll check it tonight when I get home.

othrwise id say wire the remote in line with the fused ignition, i.e. the amp turns on when the deck turns on, i believe that would work, otherwise try installing a switch, i have that in my car to control the amp on/off whenever i want to, id recommend that

In my opiion the remote  wire from the amp should be hooked to the remote turn on wire from the radio which is blue with a white stripe, the power antenna  wire which is blue, should not be hook up because its loses power when u switch sources and should lose power when the cd function is on Jamie Jackson

*CRIMPING AINT EASY*