Are you using ext3 as your file system? At http://www.zip.com.au/~akpm/linux/ext3/ext3-usage.html
, they do recommend disabling file system checks for ext3. It can be done with:
tune2fs -i 0 -c 0 /dev/hdxx
If you turn off the auto checks it's recommended that you periodically do manual checks.
Are you having a problem with the file system checks?