The RCAs you're using from the LOC aren't the same set that are coming from the headunit obviously - RIGHT?
So I say try a new set of RCA from the headunit first.
[shrug]
Why skip a simple step?
Okay. I really REALLY don't want to sound like a jerk, but I've said this at least a dozen times already.
Step 1: RCA's are going from my amp to my head unit. Like I said, I'm not getting the output I should.
Step 2: Pop the deck out, unplug RCAs, and take the RCA ends that WERE in the deck and go back to the trunk with them, and plug them into the LOC.
Step 3: Turn on head unit, magically I get great sub output.
Conclusion: I have one pair of RCAs. They are used in both scenarios. This concludes the RCAs are NOT damaged or bad in any way shape or form.
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Going back to a different route, I kind of thought about something. I asked my buddy here at work who used to work for an installation company so he dealt with problems like these. He said he's completely stumped, but the fact that 3 decks have now acted the same way he said sounds like there's something miswired within the actual vehicles harness.
To test his thoughts on this, I figured this is what I could do.
My original head unit, aka head unit number 1 (I've tried 3 now) is now in my girlfriend's car. What I'm going to do is turn my car on so the alternator is running and the remote wire kicks the amp on. Then I'm going to put the RCA wires from HER head unit to MY amp. That way, her head unit is the "brain" that will be sending the signal to the amp... while my head unit turns the amp on being that the remote wire will be activated.
Conclusion: If my old head unit in her car works, which in my car the preouts didn't, then something is beyond f*cked in my car.