"ipconfig/flushdns" actually should have a space in it "ipconfig /flushdns"
The directory/directories where DOS commands reside must be where you are located to get them to run, unless they are in the PATH statement. How that works in 2000/NT - don't know - but in the 9x variants, that 'set PATH' statement in the autoexec.bat is where it tis set up.
The firewall seemed a likely suspect too. If I'd been sitting at the machine I would have prowled the settings and noticed the sort of thing Teresa mentioned eventually, but perhaps the reinstall fixed that anyway. If it had not deleted your personal settings - and some uninstallers leave those files, then reinstalling it would have only picked up the settings and you would not have had any changes.