Do you have any software running in the background? If so, first shut them down.
Then run Disk Cleanup prior to running scandisk. Now run Scandisk and then defrag. Should clear up the system freezing up. A note here is that I have NEVER been able to run scandisk while running any anti-virus software. Especially McAfee.
There is another scenerio also, that your computer may be playing host to a worm called W32.HLLW.Bymer. Other names for the worm are Dnet.Dropper or W32/Msinit.
The following procedure can be used to check the presence of a wormup by using the startup tab of the Msconfig utility to search for either the Msi216.exe or Ms216.exe files (which may have been loaded into your computer).
To perform the preceding search, do the following steps: click Start, click Run, type: msconfig, and then click OK. Click the Startup tab and search for an entry that resembles the following example:
Name = msinit
Data = C:\Windows\System\Ms216.exe
Data = C:\Windows\System\Ms216.exe