Scandisc anomaly in Win98se

I have been getting warning messages that there is a problem with Explorer, so I ran scandisc in Safe Mode, in which the only program running is Explorer. However a message comes up: "Scandisc has restarted 10 times because Explorer or another program has been writing to disc." In other words, the scan cannot be completed.
I've run AVG and A-Squared, and they say I don't have a virus. Any suggestions, anybody??? The only ACTUAL problem I currently have is that Windows Media Player refuses to play, and others like VLC don't operate properly or do so sporadically, which is vewwwy iwwitating.

 

Is it possible that I have a trojan/spyware?

 

Thanks for the suggestion, but I don't have a screensaver.
I might mention that when I press cntrl/alt/delete, the only program showing as running is explorer. Could there be another installed program running but not showing?

 

It's been a long time since I used 98 but after it gives you the warning don't you get an option to continue anyway without any further warnings?

If not try this, I would just do 1 + 2 and see if it completes. Or just use scandisk /autofix to fix all errors without doing the full surface scan.