Well it's an issue that's plagued me for a while, since the last time I accidentally fixed it to be precise. This time however I'm making a note of what I did so that future me, and possibly anyone reading this article, will know what to do when this problem rears its ugly head again.
What we're doing here is setting what I'm terming a phantom display, similar to the phenomenon of phantom limbs. Basically, Windows 7 wants to change settings depending on what it thinks is plugged into your video card, nothing or something, so you want Windows 7 configured the same for an empty port as for an active display. Below, step 7 sets the phantom display and step 13 sets the physical display.
0. Install most recent graphics drivers and reboot after doing so. This is critical.
- Physically disconnect the secondary monitor that you wish to make persistent
- Boot the computer with the monitor disconnected. If you've already booted with the monitor connected then reboot now.
- Right click the desktop and click "Screen resolution"
- Click the "Detect" button in the top right corner
- All available inputs should appear as grey boxes with monitor numbers in them
- Select the one you want to make persistent, probably #2 if using VGA/DVI
- Set desired resolution and move monitor to desired location
- Change the box that says "Disconnect this display" to "Extend desktop to this display."
- Click OK
- At this point your secondary monitor is persistent but still unplugged
- Reconnect your secondary monitor
- Reboot
- Reopen screen resolution and repeat step 7
- Congratulations, you're done
Tested and verified on a Nvidia GeForce 9800 GT, your mileage may vary.
9-6-2013 edit - Nevermind, booted up today and all my icons were back on the main desktop.
9-7-2013 edit - I was too quick to call this a failure, it worked 100%. The failure appears to have been caused by a video driver update. Repetitive cold boots with and without the monitor connected have consistently demonstrated the desired functionality of Windows accepting a persistent secondary monitor is connected even if it can not detect it. Added step 0 above.