One of the reasons I could think of is that you have a Today plugin that somehow needs to access the Microdrive for some information. And because the MicroDrive is not initialized when that plugin does its thing, it will automatically create a folder called MircoDrive in internal storage. Did you do any soft reset between the hard reset and that MicroDrive2 appearing again?
In my case, I moved the Messaging folder from \Windows to MicroDrive, and I enabled the Messaging plugin on Today's screen. Naturally, this caused the actual MicroDrive to be recognized as MicroDrive2 (for reasons stated above), and I had to remove that plugin, and do a soft reset to clear the problem.