@gfs
The issue reported above was addressed by the developers, confirmed as fixed (via email) by the original poster (robertcoldwell) and the bugfix was included in Juicebox v1.5.0 (which was released on 24 May 2016).
It certainly seems strange (though not impossible) that the problem would crop up again over a year later in a different version.
One thing I notice which could be causing layout problems is that there are several HTML errors on your web pages, including stray and unclosed <p> and <span> tags (and extra double-quotes alongside certain <div> attributes). Also, your gallery <div> containers are inside <p> tags. (A <p> element should not contain another block-level element such as a <div>.)
Try validating your gallery web pages with the W3C Markup Validation Service and fix the errors reported.
Once the code on your web pages validates correctly, the web pages should be rendered with greater consistency and predictability across different browsers and devices.
Unfortunately, I do not have access to an iPad Pro so cannot check your web pages in such a device myself.
If, after fixing the HTML errors on your web pages, you still see the problem, then I'll happily compile a report for the developers who will investigate further but it would help to have as much information about the problem as possible so please let me know the following (if you can).
(1) What version of iOS was the iPad Pro running?
(2) What browser or browsers (Mobile Safari, Mobile Chrome or any others) did you see the problem in?
(3) If you can gain access to the iPad Pro again, please provide a screenshot of the problem (and let me know which of your galleries it is from) so that we can see exactly what you are seeing.
(4) Also, if possible, please let me know if the problem occurs in any of our demo galleries here.
Thank you.