Do you use any programs other than iTunes such as SharePod? If so, just reconnect and disconnect through the program.
Apple specifically tells you to use iTunes.
Also, the only purpose for the "remove hardware safely" button is to check to see if anything is writing to the disk. If you're not transferring any data it can be removed normally. In years of computing, I've only used the safely remove hardware twice.
Reconnect. If you still have problems, back up all your songs and other data and re-install your firmware. The glory of Apple is they lock down your devices so much that it's seriously impossible to mess up the bios.
I just now realized I've had a typo in my signature for the past 3 years.