I just installed VirtualBox on Windows 10 x64, loaded a Linux Mint VM (17.1), and I'm able to use the Yubico apps (NEO Manager, Yubico Authenticator). The only thing I did was install the VirtualBox Extension Pack. Perhaps it's the host OS you're running the VM from?
After installing the Linux Mint VM, I...
(1) updated with
Code:
sudo apt-get update
(2) added the Yubico PPA with
Code:
sudo add-apt-repository ppa:yubico/stable
(3) updated with
Code:
sudo apt-get update
(4) installed YubiKey NEO Manager with
Code:
sudo apt-get install yubikey-neo-manager
(5) installed Yubico Authenticator with
Code:
sudo apt-get install yubioath-desktop
(6) installed pcscd with
Code:
sudo apt-get install pcscd
(7) added the udev rules and patched libccid with
Code:
sudo sh -c 'wget -q -O - https://raw.githubusercontent.com/Yubico/yubikey-neo-manager/master/resources/linux-fix-ccid-udev | python'
(8) restarted Linux Mint
Both of the apps see the YubiKey and work now. The same steps would work in Ubuntu 14.04 +: