It sounds like your own custom elements may somehow be overlapping the navigation buttons (and that you might need to raise the z-index of the navigation buttons). However, one problem seems to be leading to another and things seem to be escalating quite quickly.
It might not be your ideal solution but it would be much easier to compromise and use the gallery's own Expand Button (on the Button Bar). You can have the Button Bar be positioned in the top-right of the main image (rather than the top-right of the gallery) by setting buttonBarPosition="OVERLAY_IMAGE" (in JuiceboxBuilder-Pro's 'Customize -> Button Bar' section).
Rather than apply z-index values to many elements (both your own custom elements and gallery elements), you might like to try changing the value of imageClickMode ('Customize -> Main Image') from its default value of NAVIGATE (where clicking anywhere on the left or right side of a main image will navigate to the previous or next image respectively) to NONE (where clicking only on the navigation buttons will navigate through the images).
This might help.
If you like, please post back with the URL to your gallery so that I can take a look at the problem for myself and hopefully help further.