Here are two more suggestions that might help.
(1) Rather than using the default setting of expandInNewPage="AUTO", try setting expandInNewPage="TRUE" (to always expand the gallery from the Splash Page in a new page of its own) or expandInNewPage="FALSE" (to always expand the gallery on top of the embedding page). You might find that one of these settings works. (You can find the expandInNewPage configuration option in JuiceboxBuilder-Pro's 'Cuistomize -> General' section.)
(2) Also, when nesting the gallery within parent containers and giving your gallery percentage dimensions, it may be necessary to ensure that all parent containers have dimensions specified via CSS.
For example, if your gallery has a height of 100%, then Juicebox needs to know what its actual height should be 100% of. If the gallery's parent container does not have a height specified via CSS, then Juicebox may not be able to determine the gallery's actual height.
Please see this note regarding Using Percentage Heights.
Hopefully one of these two suggestions will help.