Hi, and welcome to the board.
When you say you have used "config.sys", do you mean
msconfig, the system configuration utility?
In msconfig > startup, Explorer is not a file which is loaded. However, once the desktop loads and you do a ctrl-alt-del, you should see it, systray and other startup applications.
If you have not used msconfig to troubleshoot, or not used it thoroughly, read the "troubleshooting startup folder" section of the link below.
Run msconfig, click the startup tab and remove the checks for everything but scanregistry and systray. See if the problem still occurs, and selective re-enable items until you find the one causing the problem.
http://support.microsoft.com/support/kb/articles/q188/8/67.asp
What errors is scandisk reporting? Scandisk will normally run after a bad shutdown, but it doesn't do a "thorough" scan unless you run it independently. You should probably do that and have it "prompt for errors" rather than automatically fix, so you know what is going on.