Hi Byron
a bit late to this, but in the past it was possible to have have QT (and probably also FCP) generate mov files with multiple Prores flavours in one file, so a file can contain a Prores444+HQ+Proxy at various points. And with the newish native Prores reader in Adobe there can be trouble reading those files. The exact same can happen with DNxHD files generated from Avid MC using the video passthrough export option (Same as Source) and the native DNxHD/HR reader in Adobe.
I havnt seen this in a while so i dont know if it has been fixed or i just havnt encountered these files recently. But this is my educated guess you are seeing here.
Robert