When you tested with PDVD13 where you running on a different drive/location? PDVD should not be able to read a larger than 2TB drive either if it is a drive setup issue. See this Microsoft article http://support.microsoft.com/kb/2581408
Who said its a drive setup issue?
Its very well possible that a specific piece of software simply doesn't work above 2TB, for the same reason you need a specific setup to make them work properly, but otherwise unrelated.
In any case, Microsoft designed the DVD Navigator to play DVDs from an optical drive, so the 2TB problem is most likely not a case they really had in mind.
Sadly, MC has to rely on the DVD Navigator because implementing your own would be month of work, in addition to the license costs for even getting access to the required documentation to do it.
You could of course try to bug Microsoft since their own application also fails, but i don't have much hope to be honest.