Thanks for the suggestion dzintchy. That's pretty much the settings I'd been using, except for ticking on "Ignore Object Export Settings" (I didn't tick that since the objects in question don't have any Object Export Settings) but I ticked it on and output another file.
Don't have access to the iPad today but looking at the images in Sigil the middle one is half the size of the other two, with their sizes being defined in the img
tags. I have discovered since my post yesterday that iBooks has a bug that means it ignores size attributes on the img
Unless anyone comes up with a great workaround I'll have to unzip the ePub and check/adjust all the image files to make sure they are consistently sized.