Okay I have this problem that has bugged me for a long time, and I don't know how to resolve the issue.
I have some footage that is 720px X 480px with a 0.9 pixel ratio. When I look at that video in the program monitor, the size on screen is 640px X 480px. How did this happen?! I want to maintain the 720px X 480 px. I tried to set the pixel aspect ratio in the project settings, but it is inactive. AE allows me to do this very quickly and easily.
Yes, and that fixed the source monitor, but not the program monitor.
I read the help file and it explained that to change the overall project settings pixel aspect ratio, you have to create a new project file with the settings you want (using custom from the dropdown), and then import the problematic project. It fixed the problem.