I have had this issue before. My kobo is running the 1.4 firmware. I can only remember this happening twice before and only with one book. It is an ePub version (previously PDF) of The God Delusion. When I would power on the unit from a completely shut down state, it would bring me to a page or two before the page I had left off.
I just grabbed my kobo to test it out and it resumed on the page I actually left off on....sneaky sneaky kobo.