The first line in the start() function is:
$("select, embed, object").hide();
And the last line in the end() function is:
$('select, object, embed').show();
This forces all select, object, and embed nodes to be displayed when the lightbox is closed, regardless of their display state prior to lightbox being opened. This is causing problems specifically with the popular Responsive theme, which dynamically displays dropdowns for navigation on mobile devices but hides those dropdowns for larger displays.
By commenting out both of those lines, the problem went away. I assume those lines are there for some reason, though. What is the purpose of those lines?