I have similar issues:
a) HP laptop 6910p, ATI graphics
b) 90W docking station (the one that connects underneath the computer)
When I boot up up, the docking station display comes up, but the driver thinks that the system has two monitors and it creates an extended display. The gnome (or KDE) login shows up on the laptop screen (but I have closed the laptop lid of course since its in the docking station). I have to do a blind Enter then a blind enter my password. No login panel appears on the docking station screen. The docking station display is significantly larger.
For some reason, fc16 thinks that it should be an extended screen versus one screen or the other.
Once I login, I get one screen.
I have played with the fc16 gnome3 "display" control panel but it is hard to figure out how to use it because it keeps jumping around on me as to which screen is active or not.