My Windows laptop wants to repair my phone, but my phone is happy
I had that on my old HTC Magic a couple of times, it is supposedly down to not properly doing the Eject Disk bit in Windows and Unmount drive bit on the phone before unplugging it.

After it had annoyed me enough times by asking me to repair the disk every time, I unplugged the micro-SD card from my phone, put it in a USB SD card reader, plugged that straight into the PC and let Windows run the repair. This time the repair completed successfully, and after plugging the SD back into the phone I didn't have any more problems with it (for a few months at least).