if i remember right, you need to drop into single user mode and run fsck manually
try this in single user mode
e2fsck -v -y <partition>
that is only if you have an ext2 filesystem
this comes from my slackware startup script btw. according to the man page the above will be more verbose (-v) and will answer y to all questions (-y)
so when it detects an error it will just go ahead and fix it (that's what i assumr, i have never had to use it myself).