Originally Posted by DaleDe
I think the gray margins are due to the aspect ratio of the document you are viewing, not due to the iBook. It is flush with the left and right edges. To maintain a correct and accurate aspect ratio you will occasionally see this sort of thing. I have some PDF's that have gray bars on the left and right sides as they happen to be a bit taller than they are wide.
That makes a lot of sense... In fact, I should have realised it was the aspect ratio myself.
Thanks for your help! I guess it's time to just deal with it and pick my favourite reading app!