I found a simple workaround for the time being from a Cinnamon bug report. Just do this:
"A hacky fix for this is to go to Full screen mode, which makes the menu work correctly, even after changing back to normal view."

So just transition the IDE to full-screen with Alt+Shift+Enter, and then back again with the same keyboard shortcut and your problem is fixed until you open Netbeans again. The next version of Cinnamon should fix this by reporting it's self as Mutter to the Java virtual machines until proper support is added for Muffin.