Not sure why you’re not seeing it (probably an alpha channel issue) but you should render it at 720×486 in AE. Why would you render it at 720×540? I realize that is square, but AE takes care of mixing all the square and non-square issues. You should always work in AE at the native format you’re creating for for best results. If you must work in 720×540 (still don’t know why) then your last step should be to place that comp into a 720×486 comp before rendering. Avoids field mush if you’re using fields. If you’re not using fields, wouldn’t you want AE to do the scaling instead of FCP? FCP isn’t exactly known for scaling and subpixel rendering quality. Ugly.