I have seen these problems also. There are portrait/landscape settings in the driver, and in AutoCAD. Same for pagesize, and other settings. It's difficult to figure out which settings rule.
Are you plotting directly to the PDF system printer, or have you configured a PC3 file?
For the users who create PDF's here, we have started using CutePDF and these users are not having these problems any longer.
I know that doesn't solve your issue, especially since you already have Acrobat. Maybe some other suggestions will be posted.