The Op has done a great job of explaining his problem. We aren't doing him much of a service so far.
The amp is a 2 channel. First question should have been how it is wired to both subs, stereo or bridged? A diagram of exactly how it is wired will help
The RCA's are probably fine based on the OP's tests. If he can get either to work, they are ok.
The LOC wiring to the vehicle wasn't clearly defined. Which speaker wires? Rear? Verify those connections, even swap them to test both channels of the LOC.
Many Honda's have Active Noise Canceling. This wrecks havoc when you add subs. Verify if you have an ANC system and bypass/defeat it if you do.
I too have seen this problem before. Usually is the result of phase/signal polarity. If it was louder with either left or right RCA, I would suspect sub wiring. If the right doesn't work then it seems to be before the amp and the right RCA is pulling the signal down. Maybe the right LOC input is reverse polarity.
I've never had to draw any sort of diagrams, and I don't have a scanner, so I suppose I'll have to take pics. Here is what I have hooked to the amp (which is screwed into the sub box):
The speaker wires are hooked from the box to the amp.
The Power wire is hooked straight from batt (which an inline fuse on it) to the power terminal on amp.
Ground is running from metal in trunk to ground on amp.
Remote lead is running to my fuse box under my dash I believe, hooked to an acc fuse.
The LOC is tapped off the right rear 6x9. It has the 2 females (one of which doesn't seem to work, even by itself, not when BOTH are plugged in on both ends) that I have the accompanying RCA cable plugged into that are plugged into the line in on the amp.
I assume its stereo ????
I don't believe I have any kind of ANC. I've had subs in this car for 5 years, and only recently noticed that it does this. But again, I've never really looked or checked because I've had more than enough power coming from my old Kenwood. In fact, i'll post a picture of where I had my Kenwood amp set on the gain.
It seems kind of how you describe, as though that right LOC RCA when plugged into both LOC and amp BRINGS DOWN my signal. Its stronger if I just leave that "dead" one unplugged at the amp. But it sounds kind of muddy, its not as clean.