I remember a comparable discussion somewhere in these forums. That PC was connected to the internet by cable, and somehow the internet or the cable modem knocked on the door regularly causing this message. Disconnecting the modem (adsl might do the same) during the scandisk was the solution here. I won't take the trouble to search for the discussion (might be difficult) so you can read it yourself, but it's so easy to try that I would start with this.
If that isn't the cause find msinfo32.exe (mine is in C:\Program Files\Common Files\Microsoft Shared\msinfo folder) and run it (can be done in Safe Mode also). Post the list of "Active Applications" so that we can see if there is anything suspected there. Most, if not all, will be trusted Windows components, but if that are really the only one (and a modem is excluded) you wouldn't get this message, one should say.
Hope this helps.
When i ScanDisk C Drive in SafeMode (WIN98SE)I frequently get, "ScanDisk has restarted 10 times because windows or another program has been writing to this drive. Quitting some running programs may enable Scandisk to finish sooner". I'm in SafeMode and have no programs running! what's this about and houw to correct it?