Fixed it
Inspired by bojan's comment I thought to hook up the DEC motor to the RA instead, to see whether it works still, since I know the RA is good.
Turn out it does, so the problem isn't the motor, and it is unlikely to be 2 bad controllers, so the left the pass through being broken.
As I went to take the RA assembly apart, I noticed there was a speck of conductive paint on the DEC connector, probably came off the socket. That's when the penny dropped - the fleck was shorting 2 pins, so it was probably shorting 2 adjacent phases together, which also explains why it works with a high slew rate!
I brushed the fleck off, checked other connectors for similar issue, found none, and plugged DEC drive back in - viola! Worked like a charm!
There is a lesson to be learnt here: keep your connectors clean! If I had paid more attention to the connectors, I would have been up and running the first night, instead of nearly a month later!
I bet the skies will be cloudy tonight though...
Cheers,
Steve