If it's only happening on bootup, you you might try running a scandisk check. You might have some twitchy bits on the drive that are causing problems when a core system function is loaded.
Right-click on the drive in My Computer, select 'propterties', then 'tools', then under 'Error Checking' click 'Check now'. Check both boxes and then 'Start'. If it's the system disk, you'll have to reboot. You should also back up before you do anything to the disk.