You must be booted in single user mode, otherwise there's no point in doing it.
However, you can also accomplish much of the same using verify and repair disc by using DiscUtility while booted from a CD, an external drive or another partition. Just make sure you use the DiscUtility which came with the OS you're running.
Your problems with IE (which Harv helped you with), were probably preference or OS cache related. I don't think it was a file system issue, you'd have other problems if it were.