I had this happen several times ages ago, Windows 7 I think.
I'm not sure what I did to fix it, but I think I shut down, disconnected the secondary screen - the one I didn't want Windows defaulting to on boot/waking - then booted and reconnected the other screen after Windows had loaded then checked which screen it thought should be the primary one.
I've a feeling that the problem has something to do with which screen had focus the last time Windows was shut down or put to sleep, it then recalling that screen as the one to activate first. Though that's a guess on my part.