And the source file is 1920×1080?
When you say you AMA-link and then export Same As Source, do you first consolidate at any point (methinks one cannot export AMA-linked sources Same As Source).
Where are you determining that difference? Source/Record monitor? Full Screen Display? Quicktime Player?
In 6.5 and later, ProRes is a native codec, so if you fast import it or AMA-link & consolidate it, then export Same As Source, not a single thing about the source will be changed. This would be 100% transparent.
The Custom options in the QT export just reflect whatever Quicktime codecs are installed on the system. The Avid QT codecs are just that, Avid JFIF and DNxHD codecs for use in Quicktime.
Generally speaking it is much smarter to export a Quicktime Reference or Quiktine Same As Source, then use a 3rd party encoding application (MC comes with Squeeze, but there are many more options). MC is not an encoding app, it just uses the QT engine that I don’t think is the greatest.
And ypu should then export the result Same As Source. Don’t do a Custom export to ProRes 4×4, as it means a needless re-encode using the Quicktime export engine.
Your ‘workaround’ is the very best method. Fast too. Best because the transcode to ProRes inside MC keeps correct gamma and luma levels, unlike the conversion to ProRes 422 in the Custom Export options (which is actually just using the Quicktime encoder). Fast, because the transcode inside MC can use multiple cores.