Are you plotting via Acrobat Reader directly?
I've had very limited success with Acrobat being intelligent and not rotating the content off the page when working with paper sizes larger than 11x17.
What we did with the troublesome ones before we started using Reprodesk, was to convert the PDF to tiff (Acrobat can do this) and either give it a go printing the Tiff itself, or insert it into an Autocad file as an image, and plot it that way.
Certainly not the best solution, and not knowing more about your plotter than I do, most likely much more work than what is needed.