I'm another who always powers my ereader (touch) down every time i finish reading. the powering off and on doesn't seem to ever decrease the battery.
you asked if it could be the kepub ... two things to consider. one is how big a file it is. the few times i've had strange battery draw, it's been due to the book i was reading being a large file.
second, when you put it to sleep do you leave the book where you left off, or do you return to the home screen? that might make a difference.