First, make sure you have installed Java version >1.6.0
Next, download the files "Installation Package for Windows", and "Codeloader (Java)". Unzip the driver-win-imote2.zip in a new directory.
After attaching the new flashed Imote2 device, press button on the device within the first 3 seconds. Now the boot process of the device is halted and is waiting for an image and letting you install a driver in Windows. Follow the driver installation wizard, and select location of the prior unziped .inf file.
After the successful installation of the driver package, you can use the codeloader to upload new images.

After startup of cygwin, please check, a Java version > 1.6.0 is running, by typing java -v. If this is not the case, check by which java where this version resides uninstall/delete it and install a new version. If a new version is present in the Windows installation directory, cygwin will use it.
Copy the downloaded jar-file to /opt and copy the file codeloader.sh to /usr/bin
Now you can flash the Imote2 by executing codeloader.sh with the appropriate parameters