This is the FormCentral forum, You may want to check the Acrobat forum: http://forums.adobe.com/community/acrobat
I believe the orientation that you initially scanned in your pages will be the orientation saved in the PDF file. Now, you will need Acrobat to manually rotate the specific-page-orientation. Depending on which version of Acrobat you have, you should be able to either change the view of a page by selecting 'View/Rotate' or 'Documents/Rotate Pages'. Acrobat will not rotate it for you automatically after scanning.