I managed to get this sorted yesterday. I took the wiring that was going to the crossovers in the dash out from the amp, and the sub was working fine and amp was running as it should.
This then led me to believe something was up with the original wires from the car, so I used some wiring to go from the woofer out terminal to the woofer in the door cards, and low and behold, it worked! So did it with the other side too and it was fine.
I've now completely eliminated original wiring so now my system is like this:
Headunit > 2 x RCAs (one for speakers, one for subwoofer) > speaker wiring for sub straight to amp > speaker wiring from amp to crossovers > wiring directly from crossover to speakers in doorcards > tweeters directly to crossovers in the dash.
Sounds a bit punchier than before too, I suppose it's because I'm using the 4awg cable now instead of the 8awg?