If you use rotate view you will be given the option to also rotate the center marks. Uncheck that option and they'll stay parallel to the page.
Another way would be to use the connection line option when inserting the center marks prior to the align/rotate, which should force the center marks to be aligned to the long axis of the part.
That did the trick. I had to laugh I was going over the drawing packet again and was wondering why this part wasn't done and then I remembered...