arkanabar,
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.
<menu>
<!-- 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/) -->
<file>/usr/share/lubuntu/openbox/menu.xml</file>
<hideDelay>200</hideDelay>
<!-- if a press-release lasts longer than this setting (in milliseconds), the
menu is hidden again -->
<middle>no</middle>
<!-- center submenus vertically about the parent entry -->
<submenuShowDelay>100</submenuShowDelay>
<!-- this one is easy, time to delay before showing a submenu after hovering
over the parent entry -->
<applicationIcons>yes</applicationIcons>
<!-- controls if icons appear in the client-list-(combined-)menu -->
<manageDesktops>yes</manageDesktops>
<!-- show the manage desktops section in the client-list-(combined-)menu -->
</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.