so lemmie see here you got a 4 chan amp. running 1 set unbridged and one set bridged seems to me the OHM load would be WAY too low and ur amp is simply going into a thermal protect/overload protect

well i think it may be a couple things. first off how is the sub channel wired. do you have 1 or 2 subs are they ran in series or paralel and what ohm are the speaker and how many voice coils. i agree you could be simply overloading the sub channel and a simple rewire may solve that. but the thing that is wierd is the way the fronts are acting. how many pre out are you using? if you are using two then maybe they got switched around. i have seen this when people try to use a rca cale bundle with 4-6 leads in it.

make a diagram of all speakers, and the OHM load they have on the speaker itself, then JBL'* specs.

most 4 channel amps are 4/3/2 channel acceptable

you can run a set of interior speaks off 2 channels, while bridging the the rear two to run 1 sub. its a very common application. i'm guessing you have crossovers / outputs adjusted wrong and its reading one side should be bridged while the other isn't. make sure there'* a 4/3/2 config available on it

Ok, Two 5.25" audiobahn (save the comments) components in front - 4ohm impedance
120 watts rms, Frequency 35hz-25khz, 15 oz magnet, 90dB sensitivity. These are run using line level inputs (off of stock stereo).

In the rear I have spliced into the rear speaker wires (both left and right) and again run in using line level inputs.

The sub is a pioneer TS-W33C, 150 watt nominal (450 max), 12", 4 ohm impedance, 91 dB/W sensitivity, 20-4000 hz frequency. I have it bridged as it is labeled on the amp itself (negativ far left, positive far right with two empty in between).

The amp is a JBL 80.4 --

Power Output 4 ohms 40wx4
Power Output 2 ohms 80wx4
Power Output 4 ohms bridged 160wx2
minimum impedance - 2 ohms
frequency response 10hz-50khz
input sensitivity (rca type) 250mV-4V
THD + Noise (4 ohm) 0.05%
signal-to-noise >100dB
maximum current draw 43 amps
fuse requirement 20Ax2

Here is something else. Some amps will not work correctly, or will destroy itself, the sub(*), or speakers. They are setup with the switch to choose low full or high output. Subs you know are not deisgned for for full, and full range speakers are not designed for low range.

May not apply to your amp, but then again.

There are full , low and high pass filters right on the amp. I did have front set at high and rear at low.

It could be a couple of things. It could be that the rca inline boxes are going bad. Also you said you have a stock headunit. Did you cut the wires going behind the stock headunit that were powering the front speakers. I didnt see if you mentioned this so curious. If you didnt I would recommend doing so, theres a good chance you could start a electrical fire if not.

Does it work fine in 4 channel mode?

Just curious, why do you have your rears amplified instead of the fronts? The fronts need much more power, and they would give you a great soundstage if amped.

Couple more things -
1. Didnt cut the wires behind the headunit, tied in inside the door.

2. I don't have the rears amped - I spliced into the rear wires to get a signal to run the sub. The fronts are amped.

All inputs are line level, not RCA. (maybe I am misusing the term line level, but I thought it meant straght from the wire, not RCA adapters).

Haven't had any time to check things out further.