I think he's an Autobot. Not in the sense of fighting for their cause, but he may have originally been an Autobot to begin with. In the Allspark Almanac, it shows Prowl saying that Lockdown was not a Decepticon, but he worked with them often(as we all know). Then he went on to say that Lockdown features Autobot qualities....physically anyway. He covers his insignia, but it sure looks like an Autobot emblem to me. Its almost as if it was sure fire (imo, at least) that he was going to be revealed as an Autobot in season 4.