I’ve been trying to reproduce this and the only way I see this problem is if there is no firmware deployed to the board.
MFDeploy should tell you the firmware version number and assembly version numbers. Could you have a look to confirm this information please.
I think you can get this information by using the File->Connect to device menu item in MFDeploy.
The firmware update process is discussed on this page. If you plug the Netduino into the computer in DFU mode then the updater software should tell you the device type (Netduino 2 Plus).
If it says STM32 in DFU Mode then it would suggest to me that the firmware and device ID is missing altogether. It can be solved, let us know what you find.