One of the developer PC's running Windows Vista Ultimate had the second monitor stop being recognized in Windows overnight. There were no hardware or driver changes at the time, though I have subsequently updated to the latest nVidia drivers (card is NVIDIA GeForce 210).
The non-recognized monitor IS recognized during the boot sequence. In fact, only the "bad" one shows the POST or the Windows loading screen. At some point during Windows initialization after the loading screen disappears and before the logon screen appears, the active monitor switches.
When I open the Vista monitor properties window, I see my primary display and secondary display depicted. The primary one is portrayed as the regular blue box, but the secondary one is portrayed greyed-out. I have the option to "Extend desktop to this monitor", the only resolution is 800×600, and all of the advanced monitor properties are greyed out as well. If I opt to extend the desktop, the greyed-out box turns blue, when I then select Apply the screens flash as usual and I'm given the 15 second countdown to accept the new settings and when I do, everything returns to the previously broken state… secondary monitor is portrayed greyed-out again. At no point is the desktop shown on the secondary monitor.