browsers can surf fine, but programs cannot find their update servers??

windows update and many other programs that auto update cannot connect to their update servers but i am able to connect to the Internet and surf without any issues. problem started after getting infected with malware/viruses/trojans. I am not using any real time antivirus programs but have scanned with emisoft antimalware and malwarebytes. The first time i got this problem i did sfc /scannow to reinstall protected windows files and this did the trick. Since then the problem has reoccured and sfc no loger resolves this issue. windows update gives error 80072EFD when i try to update from windows. windows trouble shooter reports a problem but cannot fix it. Other programs say they cannot connect with the current Internet settings but i am unsure of how to proceed. Any help would be much very appreciated. Many thanks in advance for your responses.