Chkdsk can also be run from inside Windows, WITHOUT using cmd lines.
In my computer, right click the drive and select properties.
on the tools tab, click Check now (that's what it says on my Windows 7 install, it may be different for Win XP)
Tick both boxes and click start. (it will complain it cannot check a disk that is in use)
Click yes to the boot time scan, and restart the machine, and let it run through.
If this does not fix it, Download, install and run a program called Defraggler, it is mafde by the same people as CCleaner and runs great! I found that I had one drive I had was somewhere in the 90% fragmented range, and Windows Defragmenter just gave up, however Defraggler did a great job and bought it back down to 1~2%
All the best!