I'm having the same problem, Keith. I used the trade paperback template for Word. I am pretty good with word processing programs and I have footer information in the footer, and book text in the body of the book where it is supposed to be. When I look at the two-page view (and when I print the book in hardcopy) the right footer line is elevated above the left. Not a huge deal but I have had my test readers comment on it.
I'm about to play with it now. I'll let you know if I find out anything.