Depends which version of FMP you are working with, and how you amended the PDF
When you rotate a PDF, all you do is set a flag saying 'I am this size and orientation, but please look me this way' The file underneath does NOT change
Some versions of FMP have had problems with correctly interpreting the rotate flag so show the fuel in the original orientation.
To make this stick you have to create a PDF in the orientation you want and then rotate and insert your existing contents. It's not that difficult to write cod ego do it, but it is not a trivial task either.
There was discussion around this issue in a couple of recent threads. I suggest you take a look—
Note particularly that FM recognised an issue and has fixed it in FM14.
I had the problems in FM 13 Pro Advanced... I also thought of something like a (not taken correctly) rotate flag. I will have to see if this is stil a prob in FM 14.
As far as I have seen so far this is fixed in FMP14..