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I had this problem on the virtual box virtual machine running Ubuntu, that some times, the numpad keys worked and some times they didn't. I thought it was some bug, or some issue with the guest additions, or even that it was related to starting the virtual machine while the numpad led is activated.
Nothing like that. I though I could share the solution.
The solution is quite simple:
System -> Preferences -> Keyboard -> Tab "Mouse Key" -> deactivate "Pointer can be controlled using the keypad".
And the numpad keys work fine.
Source: https://forums.virtualbox.org/viewtopic.php?f=1&t=18023#p77983
Same problem raised when i was using Ubuntu 15.10 in my laptop.
Can be simply solved by switching off this option(mouse key).
num keypad not working ubuntu 15.10:
Hope this helps in virtual machine too.