I'm using lxpanel 0.6.1 and rarely I'm seeing that the startmenu after opening it is overlapping the panel instead of being directly above the panel.
I believe this issue is completely fixed in latest version of LXPanel - 0.7.0. Try it, please, and let us know if something is still wrong. Thank you very much.
I'm using now LXPanel 0.7.2 and have still seen this bug.