Without the controller being connected to the motor, it isn't really a valid operational test being performed on the hall inputs or phase outputs of the controller while trying to operate the controller.
I would expect that you *should* get zero signals on either one without a motor attached, but with a throttle input commanding the controller to try to run an unconnected motor, the phase signals being spewed out on the "antenna" of the unconnected phase wires from the controller, they could be received back on the hall lines as RF noise and detected as spurious hall signals by the controller.
The 5v pullups on the controller hall inputs *should* prevent this, but if the noise is sufficiently "loud" it could overcome it, depending on the design of the inputs. I've never tested this scenario on any controller.
The closest scenario that could apply is leaving the hall inputs disconnected because it's running a sensorless motor, but in that event the phase wires are still connected to a motor, and not just being antennas for the signals on them. (there is always some signal radiation from the phase wires and the motor, but in a closed loop with the motor it mostly flows thru the wires and back to the controller).
If a factory reset and the manually resetting each setting back to your normal known-working settings doesn't fix it, and all the hardware outside the PR is working normally, and the PR indicates it is getting all the correct signals into it, but is still not attempting to run the motor, then the most likely issue is some firmware bug or corrupt setting that isn't being cleared by any of the changes you make (even though you *see* all the right values onscreen to match your previous setup). (since it couldn't be a "hardware" failure of the PR in driving the motor, as it works to autotune it, and it can't be a hw failure of the PR in reading the throttle or brake, as it displays those correctly on the setup software.
If all of those are true, I don't know anything else you can do to correct the issue. At that point, either the PR would have to be replaced, or reflashed firmware and ensuring all the settings are completely cleared out, but I don't know of anything that allows an end-user to do this. The PR setup software has a "factory mode" but it requires a password to access it, which I presume must come from ebikes.ca, and I do not know what might be available within that mode.
You could try using the File - Advanced Export to create a file that has *all* parameters from the controller, including stuff you can't normally change, and either examine the resulting XML file in Notepad, etc., or send that to ebikes.ca to see if they can see anything in it that might cause this problem. I don't know which parameters in it are relevant to this issue, but there are a number of throttle, etc labelled parameters that might be involved.