I came across the same issue running FMS 12.04 and FM 12v4 clients both on OSX.
When I open the (mutipage) pdf in Preview the orrientation is correct.
If I then use a Save As and Import the pdf again, the pdf is correctly in the container.
It seems that FM does not respect the orientation of the pdf when the pdf is created (using a scanner). I have seen the same issue with photo's made by an iPhone.
Has someone found a solution for this (other then manually Save As)
Ruben van den Boogaard
Same issue reported with one of my clients taking photos with an iPhone, but if the photo was saved to a desktop before importing to the container field, it was orientated correctly. Would love to see a solution for this (apart from instructing my client to hold their phone differently!)