Clicking/Ticking noise from Stereo

I need some help troubleshooting a problem with my boat's stereo.

When my key is in the accessory position (turned to the left) and my stereo is on I hear a constant clicking/ticking noise in both my cockpit and tower speakers (approximately 3 clicks a second). (Also occurs while the boat is running, but it is harder to hear over the engine noise) The clicking is more noticeable in the left speakers on both the cockpit and tower, but can be heard all around.

The noise is constant and does not increase or decrease with volume. It disappears when I mute the stereo or volume down to 0. Fading/balance has no effect.

The installation was done by a professional audio shop here in Los Angeles, and has a lifetime warranty. I weary of taking it back to them without some knowledge of what the problem might be. Any input is appreciated.

Equipment:

2005 Mastercraft X-2
Clarion XMD3 Head Unit

Amp 1:
Rockford Fosgate P4004 running:
4x JL Audio Separates (2ohms parallel channels 1&2)
1x JL Free Air Subwoofer (4ohms bridged channels 3&4)

Amp 2:
Rockford Fosgate T8004 running:
2x Skylon Rubicon 450s (bridged 3ohms channels 1&2 left, 3&4 right)

Clarion ce-NET iPod Adapter
Clarion ce-NET Sirius Receiver

i would think ground..

Isn't a ground loop usually a buzzing noise (not ticking)?

Any chance that you're keeping a cell phone near the stereo? I don't think it would cause a constant clicking, so it's not likely, but when i have my cell near the head unit, i get a more than occassional clicking sound through my speakers. just a thought.

12v+ too close to the RCA cables?

Sounds like digital electronic noise and if it is independent of the head unit, it sounds like it is entering between the head unit and the amp or in the amp. How are you splitting the RCA's to the two amps? Are you using the front and rear outputs of your head unit? Sometimes a head unit allocates the rear to be a sub output, maybe their is some switching issue there? Are you running into one amp then out to the other throught the first amp?

Try Isolating the amps by unplugging the RCA's. If you are using the two seperate RCA's to the amps from the head unit, it seems a little strange that that would be it but try it anyway. If it goes away then it may be your routing of the RCA cables or a head unit issue. Try reversing the left and right inputs to the amps or the left right output from the head unit. See if the problem travels from the left to the right. Doing these couple of things will at least point you to the cables or the head unit or amps. Are your cables routed with power cables? That is a no no by the way.

Thanks for all the replies. I will try out these suggestions.