Windows 3.x did require the win in the autoexec to boot, but it was no longer needed with win9x. Although there have been a few computers that where hit with a boot sector virus that wouldn't boot into windows on start until you entered win.
What is getting me is the fact it is loading autoexec.bat and config.sys if it is getting to a DOS prompt. That means that either they are loading correctly, or that there is something in them preventing windows loading. Now if there is nothing in there, that means there is something else that is happening when windows starts.
Have you tried going into windows through safe mode? If you can get in through safe mode, then more then likely there is a driver or such that is causing the system to reboot.