It shouldn't affect anything outside of the actual Windows environment (i.e. a Scan Disk). Could also try doing a chkdsk if you think it may be your HDD. Can do it 1 of 2 ways:
1) Open My Computer > Right cilck your drive > Properties > Tools > under 'Error Checking' click Check Now > Check both boxes > Should say it will have to be done on next reboot. Click Ok > Reboot > Let it run through (may take a while).
2) If you have the XP disc: Boot off of it > press R to enter the Recovery console > select the OS you want to do (usually the C:\Windows\, choice 1) > type in 'chkdsk /r' without the quotes. This may take a while as well.
Ok so not really sure if it helped or not but since running the chkdsk things have been running much more smoothly. Oddly though even though I had been switching back and forth between a high graphics game and the internet when I closed the game I got a blue screen of death. Coincidence or something more sinister?