I've run Check Disk manually after booting up and found no problems. I also repeated with a surface scan and again no problems. Finally I ran Norton (Symantec) Disk Doctor which also didn't find any problems.
So does anyone know why windows wants to keep checking the drive on every boot?
XP Pro Corporate Edition with Service Pack 2 and all updates, drivers etc
Prescott 3.2, 2 GB RAM, 120 + 200 + 250 + 250 GB SATA HDD, DVDROM + DVDRW, GForce 6600 256MB