Probably Scandisk/Check Disk is enabled during start up on your PC.
However if it is running automatically then there might be various reasons,
1: IF PC is shut down improperly.
2: Bad Sectors on your Computer.
3: HD might be on the verge of corruption.
You may want to let that run and if you want to disable it then you may want to follow below mentioned steps,
Do it with the freeware version of X-Setup: http://linux4.wekanet-team.de/download/390/xqdcxsp-setup-en.exe
Download and install the program, run it, click "Classic," and on the plugins list go to Startup/Shutdown>Startup>Windows NT/2K/XP>01)Bootup Options>Boot-time Autochk Settings. In the plugin options window on the right you can disable chkdsk running on bootup for a couple types of bootups.
Go to : my computer ----> right click on the hard drive you have -----> then properties -----> tools
and see if your scan disc feature is enabled.
If it is then when your computer restarts, it will do an automatic hard disk check.
The default value is BootExecute:REG_MULTI_SZ:autocheck autochk * NOTE:
You mey want to try step 2 first and not try step 3 with proper guidence as a simple mistake can corrupt your OS. I mentioned this as part of knowledge sharing.