windows 98 is not starting automatically

I recently had a problem in which numerous system files were lost (not sure why… hard disk error? virus scans do not indicate a problem). Regardless, I have managed to at least get things running again by utilizing the SYS command, as well as manually rebuilding an autoexec.bat and config.sys (not sure why I had to do this either, but it at least allowed me to start up Windows).

Now.. . when I boot up, I get the Windows logo screen, but then it just goes to a C prompt. I can type the Win command and start Windows manually. What’s wrong here?