i have the exact same problem. BUT i used not to have it! i came out of the blue! i could use the extension with changing to primary fine and suddenly i can't. i can elaborate on this in case you can give any advice.
i have a second monitor as an extension to the right. So far, i could drag a movie in the second monitor, close the lid (which the laptop screen is my primary as i want it to be) and the second monitor could still be an extension. Suddenly, that changed, now whenever i close the lid my second monitor becomes primary (which is annoying). when i open the lid, it goes back to being an extension to the right but the identification numbers are upside down, meaning that the laptop screen became primary again but No. 2 and the second monitor became extension (as it was) but No. 1. I can't find what's wrong with that. The only thing i can think of is that i tried to force a game to open in fullscreen to the second monitor while having plugged ps3 controller (with MotionInJoy) and i got a BSOD. I think that after that it happened. I didn't take seriously the BSOD because i had it a couple of times with another game and with no second monitor. I uninstalled the game. I re-installed it today and to my surprise i saw that when i launched it, it started in fullscreen mode in my second monitor. somehow is like it remembered it even though i completely uninstalled it. i tried forcing it the same way to play im the laptop screen but nothing came from that. When i say force i mean that i changed it to windowed mode, dragged it to the other monitor, and then changed it back to fullscreen mode. When i first installed the game it worked (and probably messed my monitors), now that i tried to do the same but backwards hoping it will undo whatever happened, it just crashed. tried to open it again but it started in the second monitor as before. Sorry for the long post! Any ideas? I searched all over but nothing seems to help or being at least relevant to my case. Thank you in advance and sorry for the long post again!
i have hp laptop with win vista.