Problem with Scandisk

[JohnE]

A friend of mine asked me to look at his computer which had being playing up for about 2 months. Needless to say it was riddled with spyware and general malware. No actual viruses but the usual autodiallers etc.

I've managed to remove everything but there's a strange problem left over.... If I try to run Scandisk (this is under Windows 98, BTW) it just seems to get stuck in a loop, repeatedly stopping and re-starting. Sometimes the progress bar gets about 10% of the way along before re-starting, sometimes as much as 50% but it never gets much past 50%. If I run Scandisk in Safe Mode, everything's fine - so I suspect that Scandisk itself is okay. Something must be preventing it from running properly in normal mode.

I wondered if this might be a side effect of one of the malware apps. Scandisk was misbehaving in exactly the same way before I removed anything but it's still misbehaving afterwards. Has anyone else come across anything like this?