I have the same problem, unable to autenthicate account with minecraft.net. Works fine with minecraft.exe. I've tried removing the folder from %appdata%, checked java is correct and reinstalled, literally terminated every application and I can (including antivir and firewall) and tried some solution including mineshafter (not sure if I did it right or if it even should help). Nothing helps. Any ideas?
E: Running win7 64-bit and the minecraft I own is legit.
E2: Got it to work by logging via email. I thought you login with the username? Was I wrong? Lulz, works anyways.