Virus removed, web browsers not working.

Hello, I recently got hit with some trojans the other day. I downloaded MalWarebytes and removed all the threats. Went to IE, FF, and Google Chrome and took off all the proxy settings that were added. (I've done this before). Browsing worked fine on each one, no issues. Did a restart to be on the safe side, and then that's where it all went downhill. Proxy settings aren't checked, yet it still says "page cannot be displayed/cannot connect to server". i restarted the computer, ran it in Safe Mode with Networking, and the browsers all work. Slower than usual, but connecting nonetheless. I'm wondering if there's still traces of the virus left? I've scanned more than once, even in safe mode, nothing detected. Could it be a registry issue, maybe something was edited by the trojans? Any help is appreciated.