Hi!
I don't believe there is any specific issue to multisite. At least I did not reproduce such issue. However, two bugs related to navigation menus have been reported. See http://wordpress.org/support/topic/menus-doesnt-show-and-not-saved-in-theme-settings-multilingual-site
So maybe the fixes are for you too. Could you try the development version (1.5.0.3)?
http://downloads.wordpress.org/plugin/polylang.zip