z-index:3was added to the ./deps/nitrogen/src/elements/layout/element_lightbox.erl, so it will look as follows:
-module (element_lightbox). %... skipped ... render_element(HtmlID, Record) -> Panel = #panel { class=lightbox, style="position: fixed; top: 0px; left: 0px; bottom: 0px; right: 0px; z-index:3; " ++ wf:to_list(Record#lightbox.style), % ... skipped ...
Should the fix be applied to the very Nitrogen trunk? It seems reasonable.