OK Steve
The problem seems to be (referring to this circuit diagram
https://wiki.batc.tv/images/5/5b/PdFM_V2_Sht_1.pdf) that the signals on J01 pins 1 and 2 (which you have measured at 1.5v - the value I would expect if they were alternating between 0 and 3.3v from the PI) are not causing any change in the voltage at the output of the opto-isolator (pin 5 of U01). This is the 4.53V that you measured at the junction of R03 and R09. The same seems to be happening for the Q channel.
As a test, you could disconnect J01, so that RPi is isolated. Then connect J01 pin 1 to ground (it is not grounded through the PCB) and J01 pin 2 to +5v. Then measure the voltage at each end of R01 (between U01 and J01. One end should be at +5v, the other at between 2 and 3v. With the 5v still connected to J01, check the junction of R03 and R09. It should be less than 1V, rising to 4.5v or so when you disconnect the 5V from J01 pin 2.
Please let me know if this works.
Dave