I am experiencing this issue with my Nokia E71.
Each time I plug it into USB Mode I can work normally on the microSD device, but when I access the built-in MP3 player, it starts with a popup "Repairing library".
What am I doing wrong?
There's an internal library of songs and their metadata. When the device is connected in USB mass storage mode, you can add and remove song files without the metadata library being updated. The USB mass storage is a block device and the phone has no visibility to the filesystem level operations performed on it.
When the Music Player app detects that the song files may have changed, it scans through the files to see if there are changes to be updated. Nothing wrong with that, but it can take a while, especially if you have a lot of songs on the device.
One possibility to get rid of the popup is not to connect in USB mass storage mode but use PC Suite mode instead and transfer songs using PC Suite's Music Manager. That way the device can keep track of actual changes on the filesystem.
There is some noise in a few fora that having more than about 400 songs can cause this issue. I would suggest reducing the songs on it to 200 or less as a test to see if that fixes it.