That certainly sounds strange. The height of your iframe should be consistent on your web page (and determined either via CSS or by the iframe's 'height' attribute) no matter what content is loaded into the iframe.
Ordinarily, the content of the iframe should not change the layout of the parent page unless there is specific JavaScript code designed to do so and Juicebox does not contain any such code.
Your gallery looks to be a standard 100% x 100% gallery so it should fill the iframe and there is little you can do on the gallery side to change things.
From your screenshot, it looks like your gallery is filling the iframe (and everything seems to be correctly vertically centered on the page) but the iframe is not tall enough for the complete content of the page to fill your iPod browser window.
The problem seems to be with the height of the iframe on your main page.
I do not know how the height of your iframe is calculated (your web site is rather complicated).
Maybe it is looking at the content of the iframe and trying to determine the height required. Perhaps a gallery with 100% height is somehow difficult for your JavaScript code to figure out how tall the iframe should be.
Check the code that sets your iframe's height to see if you can spot any potential problems with it.
Also, please check to see if you see the same problem in Mobile Chrome that you see in Mobile Safari.
Thank you.