My LXDE installation has the unaltered lxde-rc.xml file. I don't see the behavior you describe. I can right-click the panel, select Panel Settings, and the Panel Preferences window comes up above the currently running Firefox window. I just did a diff on your file versus mine. Disregarding all the hotkeys you've enabled, the following section stands out.
<!-- You can specify more than one menu file in here and they are all loaded,
just don't make menu ids clash or, well, it'll be kind of pointless -->
<!-- default menu file (or custom one in $HOME/.config/openbox/) -->
<!-- if a press-release lasts longer than this setting (in milliseconds), the
menu is hidden again -->
<!-- center submenus vertically about the parent entry -->
<!-- this one is easy, time to delay before showing a submenu after hovering
over the parent entry -->
<!-- controls if icons appear in the client-list-(combined-)menu -->
<!-- show the manage desktops section in the client-list-(combined-)menu -->
That should be <file>/usr/share/lxde/openbox/menu.xml</file>. I didn't look at any hotkey definitions because there are too many of them for a cursory diff.