First thing to check is that the USB cable is sitting properly in the ColorMunki. The case is poorly designed and can stop the USB cable connecting properly. Re-seat the cable firmly but gently, until you're sure it's in properly.
Secondly, if the X-Rite ColorMunki software is installed, it will prevent other third party applications from accessing the device even if the main ColorMunki application is not currently running. This also occurs in all cases with ColorMunki software from version 1.1 onwards. The fix is relatively simple and is documented in the readme file with SpectraView 2. The fix is the same for ColorNavigator.
For further information regarding Spectraview II, take a look at the FAQ section on the NEC website.