There is currently a known bug whereby elements which have explicitly been assigned a CSS position are not covered by the fullscreen gallery (they should be). This bug should hopefully be fixed in a future version of Juicebox.
It sounds like this might be the cause of your problem. Please try one of the two following suggestions:
(1) Set useFullscreenExpand="TRUE" (in JuiceboxBuilder-Pro's 'Customize -> Lite' section).
... or:
(2) Set expandInNewPage="TRUE" in (in JuiceboxBuilder-Pro's 'Customize -> General' section). When the gallery is expanded, it will be displayed on a page of its own rather than on top of the embedding page.
Hopefully one (or both) of these suggestions will be a suitable solution to your problem until the bug is fixed.