There is a simpler way...
Insert the Pendrive in a MACBook or a Linux System and simply format.
The reason this has happened is somehow , the format of the pendrive has been changed to ext2 or ext4 , with A Seperate visble to windows partition of 2MB. You might able to see those partition in linux and mac
I just now had the same issue and solved it by formatting the Pendrive in Macbook to FAT format.I had made a bootable parttion repair disk in linux format ext2.
All the best!!