It's not malware/spyware because you already reinstalled your OS. You say that speed tests give you good results and that YouTube is unwatchable. Sounds like your ISP is traffic shaping your line. That can happen for a number of reasons - one of them can be that you are a heavy user and download torrents all the time so they put you in their group of people where your traffic is restricted to save them bandwidth. Tiscali (UK's ISP) does that all the time .
Give them a call and see what they say - ask them if they are traffic shaping and throttling bandwidth for certain websites