I agree with Stanley that something in the Button's/Buttons' Layer Set(s) is not being accounted for. The Layer Set is what defines each Button, and as Stanley says, will include all elements in the Button in a rectangle that includes all of them.
Can you Open your Menu in Photoshop, and post a screen-cap with the Layers Palette Open, with the various Layer Sets twirled open? That will tell us all of the elements in each Button.
Unfortunately, Ps does not show a Layer Set's bounding box, but Encore will, if you Select a Button, or all Buttons. A screen-cap from Encore, with the Menu Selected, and a Ctrl+A (Select All), WILL show all Bounding Boxes.
Good luck,
Hunt