What settings are being modified when you change the resolution on the desktop monitor for the first time?

Question

I have a web UI running on a box that can change the desktop resolution on windows 7. To do so, it shells out to qres. Pretty standard. I have its HDMI out port going into a GEFEN HDMI detective plus, in order to allow it to run headless and still be rendering a desktop to be grabbed and used for various things.

The thing I'm seeing is, on a new box, with the gefen attached, qres /l returns the correct list of resolutions, but qres /x:800 /y:600 fails to set the resolution, returning "Error, the graphics mode is not supported!" (but it should be)

To fix the problem, I can manually right click the desktop, screen resolution, set it to 1600x900, apply, keep changes. now qres will work as expected forever after. If I do the same procedure and set the resolution to max (1920x1080) apply, keep changes. the problem returns, qres fails again. in the state where qres is working, qres can set it to 1920x1080, and then off of that resolution again without breaking it.

????

My question is, what is being set when I swap resolutions manually that then allows qres to work right? My problem is that sometimes these boxes are running in a remote location, and headless (no keyboard/mouse/monitor) so all I have is remote desktop, and you can't switch desktop resolutions using RDP. So the 'fix' that's pretty simple and painless if the box is next to you, becomes pretty heinous as soon as it's remote and headless.

Thanks

EDIT:

Further investigation yielded the following: Setting the resolution using the manual desktop way to 1920x1080, then running qres /s shows 1920x1080 @ 29 Hz. Manually setting it to 1600x900, then using qres to set using qres /x:1920 /y:1080 then running qres /s shows 1920x1080 @ 59Hz.

The problem becomes most easily stated as: When a gefen is attached, and the resolution is set to 1920x1080 @ 29 Hz, qres fails to set the resolution in all cases.