It's very possible the infection you had this weekend tampered with your Internet Settings (it's very common for them to add a proxy that routes you through their servers).
Start > Control Panels > Internet Options > Advanced > Reset
If not that, then Device Manager > Uninstall your network adapter > Find New Hardware > Reboot
If you should have NTP installed and it's not showing up, then perhaps the SEP install has been corrupted/broken. I'd recommend using Add/Remove Programs to uninstall SEP, reboot, Re-install SEP.