If you are having issues calibrating the ColorMunki there can be a couple of things that can affect this process. The first thing is to make sure once the calibration is completed do not press in the center, rotary dial as this will launch the calibration all over again. This is something that users have run into in the past and can cause confusion as the device is calibrated however even though the check mark is green in the Profiling my Display, it will turn back to a red check mark until it once again completes the calibration.
Secondly, make sure that the rotary dial has indeed clicked into the correct position. Sometimes just readjusting the dial will allow a correct setting to be recognized by the hardware and the software.
If you want to manually calibrate the instrument, you can launch the ColorPicker portion of the application in Photo or the main interface in the Design software. Once this screen is open and you have connected the instrument, just select the ColorMunki icon and you now have the ability to manually force the calibration.