I can think of two things that could be going on here.
Firstly, make absolutely sure you have the buttons on the bottom orange border for portrait mode on the iPad.
Secondly, in combination with the first item, if you don't have any anchors set up in the Body of your layout, the Body will not exapnd vertically. Only the footer will. This will cause your footer to expand like you have shown in the first image.
I hope this helps. Also, if you want me to take a look in your solution, feel free to post it here and I can dive in.
(Apology for my late response)
Reduce the size of the button so that it can fit within the footer = Fail
Move all the buttons to the body and leave nothing inside the footer = SUCCESS (mean the footer height is not exploded)
Move button one at a time back to the footer = SUCCESS except the last button (extreme right, which is also the exit button)
Also remove the background image on the body = Fail
Duplicate the third button to make the fourth button = OK (see further below which is a Fail)
Since all four button and footer looks perfect, so I put back the background image on the body = FAIL (mean the footer exploded in height again)
Remove picture = Fail (strange, these four button works just 2 steps above)
Move the last button out to the body area = Ok
As you can see that there is no fix pattern for failure. I also tried putting the button on the header, and the header height exploded. The button is a simple button which simple close current window.
I have no permanent solution to this, so I place the exit button in the body area so I can move on to develop the rest of the system.
Try not setting any of the objects in the footer to be anchored to the bottom. That will keep the footer from expanding.
Then anchor the lowest object in the body to the bottom, which will cause the body, rather than the footer, to expand, still keeping the footer below it.
This is what I really was getting at. Thanks, Stephen.