I've had a look at the file and the only odd thing is that one of your monitors is running at a lower refresh rate than the other. Guess that's the one on the HDMI. Other than that, everything seems normal. Which is frustrating.
You only uploaded the main system plist and not the user plist (the one with the string of random characters in its file name). The problem might be with the user plist file but I admit it's starting to look doubtful.
Other things to try:
- It might be the screen saver. If the screen saver that you're using is not one of the standard Apple ones, try using a standard one. It may be that the screen saver is changing the resolution when it kicks in. It's unlikely but worth checking.
- It might be the HDMI. Disconnect the HDMI monitor completely, delete the two windowserver plist files and restart the machine. See if the problem is still there. If it works OK without the HDMI monitor, all you'll need is another DisplayPort cable.
- Some people have had success using SwitchResX - http://www.madrau.com/srx_download/download.html - so it might be worth giving it a shot.
- Post a question on the Apple support forum with a link back to here in the hope that someone else knows how to fix it.
After that, I'm out of ideas. But it's worth keeping hope in your heart because you seem to be the only person with this problem so it almost certainly can be fixed.