I seem to have messed up the settings and can't seem to get PT with embedded alpha or separate hsp file to work. It seems offset and/or only 50% opacity or something. I have tried adjusting the scale and those setting, but nothing has worked. Any ideas?

First, are you certain that the video is actually an alpha passthrough video? Like if you view it in flat mode, you should see fisheye circles with a red images in the small areas between the circles.

You can hover over each setting, and press the A or X button to reset the setting back to default. Make sure the opacity multiplier to set to 1 or higher (since you said it's only at 50% opacity).