A total grokking of pixel aspect ratios is what you're missing.
There is a huge difference between settings and what appears on a screen because flags are set in the encode and your players have different ways of reading those flags and yoru applications may be set to disregard or auto correct for pixel aspect ratios. So there's at least 9 different combinations of settings that can be mixed up.
There's nothing easy about this PAR stuff. Nothing. You try to learn from your mistakes. But you can be absolutely certain that the machines are displaying what they've been told to show. You just have to figure out how to make all the setting work together.
Here's what I did: I created some circles and some squares and rotated them in AE. Then I supered some text over the footage that included the codec and PAR settings in various applications like FCP, AE, Motion, Compressor, and tried to figure out where things were getting messed up. It was interesting and it led us to standardized procedures for two different acquisition formats.