Hi qm,
are you using 2 types of menu (e.g. the patchwork menu and the treeview) that might be causing this?
Anyway, for the clearing the caching, go to
BO > Admin > General and then click on "Restart DNN Application"
Or
Host > Host settings then click on "Clear Cache" &"Restart Application"
I think that "Restart DNN Application" and "Restart Application" do the same thing though.
This should clear your cache.
I hope this helps you out.
Geoff