I exported a rotoed sequence of PNGs w/Alpha from AE and opened them in PI (Mac). When exporting from PI either as a PNG seq or a QT movie with Alpha, upon opening in AE the resulting file is semitransparent--the image is ghosted over my BG. When viewing the Alpha alone in AE there is image data in what should be pure white. I know this happened in PI because I checked the original PNGs from AE and the alpha is clean black/white (no grays).
I don't know if it matters, but the rototed footage is B&W, but since there's a good, clean Alpha with it, that shouldn't matter.