This is all very good information and appreciate you taking the time to provide. I will get back to the DNxHD and see if they notice. I understand what you mean on that conversion to ProRes on a PC.
I found that when using that little GUI (the one outside of AE) - what is it, cineport or something? Anyway, for large files it would hang and I also noted that it seemed to drop frames from the beginning and end.
However, using the GUI within AE, where it converts it right there, that thing has been remarkably reliable. Knock on wood.
Eric