If you have large figures and tables that must be rotated, you should use the [lscape] class option. This enables
a pagestyle lscape and places the page numbers correctly on the long edge of the page. The option loads the
pdflscape package which provides a landscape environment to place the landscape figure in. Before the
landscape environment, you need to issue a \clearpage command and change the pagestyle to lscape, and
afterwards, change it back to plain. Schematically, then, any landscape pages should be created in the following
way.
\clearpage\pagestyle{lscape} \begin{landscape} ... your large table(s) or figure(s) here \end{landscape} \pagestyle{plain}
The landscape environment makes all pages within it landscape, so if you have multiple landscape figures in
a row, you can put all of them inside a single landscape environment. This option correctly rotates the
landscape pages within the pdf document itself, which the thesis office seems to require.