Symptom
Disk First Aid checks your hard disk at system startup time, even though your computer was shut down properly. You see a message that your computer was not shut down properly.
Solution
This issue is resolved in Mac OS X 10.1 or later. For earlier versions:
Allow Disk First Aid to check your disk, then click Done. This issue does not indicate any actual trouble with your computer, despite the message you see on screen.
Each time you start up your computer from Mac OS 9.x, it checks the disk to see if the file system was "clean" or "dirty" after the previous shutdown. If you last started up from Mac OS X and used the Classic environment, Mac OS 9.x incorrectly determines that the previous shutdown was "dirty," or improper. This causes Disk First Aid to automatically check the disk at system startup time.
Note: If you have more than one hard disk or partition, then the one designated as the Classic startup volume in Mac OS X System Preferences gets erroneously marked "dirty."