Duno if this will help you or not  but   - ive seem malware  modify  the whole entire  complete os with a backdoored forced proxy -

no matter if you edited the network settings  and removed them it still wouldnt go any where

Maybe try checking the IE  registry?  believe it or not a lot of settings done by IE does a lot of changes to the PC


Take alook here maybe?

http://stackoverflow.com/questions/13981621/registry-key-for-global-proxy-settings-for-internet-explorer-10-on-windows-8