They alternate at around 2 or 3 fps or thereabouts.
That means CHDK periodically gets liveview buffer addresses which are not in use when AFL is activated.
I have CHDKPTP installed and I can get live view to work but I can't work out how to run CHDK within CHDKPTP. If I could I would take a screenshot for you.
The liveview over PTP will help you seeing what the CHDK motion detector gets as source. You won't need to upload it, but you can identify what can be seen on the "wrong" frames (my guess: the scene before AFL activation, with some random noise).
Start chdkptp, connect the camera, switch it to record mode with the chdkptp "rec" button. Now on the camera, press the ALT button several times until the buttons start to work normally. PTP and liveview will still work, and you can use the camera manually.