So, I've decoded the packet style being used... I see two packet types:
50 00 18 48 :- is an Acknowledgement signal
53 0X LN SQ :- is data, X=?, LN=Length of data, SQ=Sequence (the sequence allows re-transmission of data - which happens a lot here, so more bad programming!)
53 is followed by data, with a 2 byte prefix (destination register?) and whatever data goes into it. After the data is a 1 byte checksum.
I've now used a 4th serial port in the microcontroller to simulate the BT chip:
Output 3 & 4 is the BT link establishment to completion, right hand side. Left hand side is the working board (both these were generated with my original smaller board - to remove any potential differences). 3 & 4 are finished at that point, it's happy at least for now.
The BT chip is linked in the middle of a 6 second pause, then output 2 says something, 1 replies (there's a difference, but I don't quite know why - but I'm not too concerned). Then there's a 2 or 3 second pause, 2 says something and normally 2 will say something else after a couple of seconds... 9 seconds pass on the broken board and 1 gets impatient, probably saying "what gives?".
The data that's expected from 2 is "01 01 02" - so register 0101=02 if my guess is correct. You can see the bottom left says 0801=Ford Falcon Bluetooth for example.
Still no closer, except I know it's meant to happen within about 5 seconds of starting the BT chip. Maybe the chip was broken, and one of its I/O data lines is meant to signal it's ready - I didn't see anything in the datasheet though :(