Sounds like the desktop is resetting to a default config or something. I would try all options like unplugging one display first, then the other, then plugging back in in same order, then back in in different order, etc. And try booting with one or the other connected (don't connect the WG until windows has booted, just leave the dongle in, mb?) Then change which display is the primary and go again :/
Next, same question as before. How does windows see the displayport-to-VGA adapter? Does it's display have a name? Either way I would then try a program like CRU to edit the EDID for whatever that display is called. Remove all the video modes you don't want and leave the ones you do. If nothing else you should be able to spoof an EDID and fake a complete monitor with CRU at 480p
If that doesn't help, you might try a program like displaychanger2/DC2. Set up your two displays so the WG works. in a command prompt, get to the DC2.exe and type - DC2.exe -create="myconfigname.xml". Then see if you can get to a point with only the WG plugged in, or just the adapter it plugs into (into the LCD?) and type - DC2.exe -config="myconfigname.xml" then without removing the adapter plug in the WG and see if it works now.
Hmm, i don't know any way to fix the desktop to a particular config, if that's even the term, and stop it reacting to hot plugging your displays. Google is telling me a clean boot might help. Or enabling base video in msconfig boot options - which makes windows fall back to its generic VGA drivers, and i'm not sure that would help.