Hi there,
I had the same problem, here is my solution:
It seems that it is a viewport issue. HTML and BODY tags get the width of the viewport when the site opens in iphone/ipad. The fancybox overlay only extends to this size as width is set to 100%.
When i set the viewport to the width of my website, the overlay spans over the whole layout.
My viewport definition:
<meta name="viewport" content="width=1040" />
Watch out: This solution works fine for a non-responsive web design.
Some infos about viewports:
https://developer.apple.com/library/ios/#documentation/AppleApplications/Reference/SafariWebContent/UsingtheViewport/UsingtheViewport.html
Hope it helps!