I know this is over a year and a half, but here, in case this helps someone else:
My guess is probably the problem with your plugin using position:fixed to create the overlay (the "darkening of the page" you mentioned), and also for the container for the largest image. Web Search Position: Fixed on Mobile Safari will give you a lot of further reading on this!
It seems that since Mobile Safari believes that βviewportβ is a whole page, not just a visible part, a position: a fixed trend does not work as we would expect. I have the same problem with another jQuery plugin that creates a βmodalβ window for me with very similar symptoms, like what you described.
I am currently trying to get around this by (A) resolving the position: fixed and changing to position: absolute, while (B) sets the height and top manually based on the entire height of the body and the scrollTop window, the jquery property. I think that a good old browser bypass can be useful here, since this hack is really needed only for this browser.
Funka
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