Strange behavior is as often the result of badly written drivers and worse freeware more so than it is badly written viruses.
That said, random hard-drive use may actually be the OS or an indexer doing stuff specifically when your computer is not busy.
Random network traffic used to be a good sign, but these days rootkits will stay fairly dormant until some point much later. When they do start sending spam on behalf of their new masters you might not even notice the extra traffic, and ISPs seem to have given up calling their clients.
Settings that change themselves back shortly after you change them, or when you reboot could have been a sign, but now some programs are just that badly written. Though OS settings should never behave this way.