File system check failed

Hi,
After using Mepis 6.0.1 for about 6 months, it failed to boot with a message something like "File system check failed, illegal bocks - use manual fsck, drive is mounted as read-only, etc."

I followed the instructions and all is well. There were three problems to fix. My question is what could have caused this? and is there something I sould be doing to avoid it?

I live in a country with very unstable (and very expensive) electricity, so I boot the computer, use it and shut it off several times a day.

Once I tried to run fsck from a terminal while logged inas root and got a message that this would be very dangerous with a mounted file system, so I didn't do it. Should I boot from the CD and run this from time to time?

Thank you for your time,
Don Jungk