You can now format a USB disk (4GB or more) in Windows by using the built-in tool called "Authorware USB Disk Format". Simply run the program, follow the on screen instructions, and you are done. This is the free tool provided by Microsoft for formatting USB disks. To check if your USB drive is properly formatted, run the 'fsck' command and see if a list of errors is generated.
If none of these are the case in your USB drive, use the Windows program to format the USB disk storage format it. It is quite simple to use. To test if the tool is working fine for you, follow all on screen instructions, and then plug in the USB drive and run the program. In one minute or so, a Windows Explorer-like menu will appear.
At the 'My Computer' window, right click on your USB drive and click on properties. Here you can select the type of formatting that you wish to do, whether it is normal or encrypted, and how you would like your USB drive formatted. Click OK when you are done to permanently format your usb flash drive and return it to it's original state.