I am using Ubuntu 13.04, a 27" 1920x1080 HD monitor, and a 22" 1680x1050 secondary monitor, and have an nVidia GeForce GTX 550 Ti/PCIe/SSE2 graphics card. The card has 2 DVI ports, and an HDMI mini port. With the monitor outputs plugged in such that the 27 only has its HDMI cable plugged in, and the 22" is plugged into the first DVI port, I experience some oddities within the system settings pertaining to desktop resolution, and display of desktop background images/wallpaper.
I previously had the 22" plugged into the second port. No real reason, thats just where I stuck it. I moved a week ago, and when setting my computer up in my new house, I had plugged the 22" into the first DVI port. No real reason, it was closer this time.
At the login screen, everything is fine, except the physical position of the screens is backwards from what I would expect. This is not a big deal to me.
Once logged in, the 27" will have the Unity launcher in the middle of its screen, and the desktop wallpaper will be set to 1680x1050. However the screen is still rendering in 1920x1080. The desktop has its XY 0,0 position in the center of the screen, and draws half the screen to the right. The other half of the screen begins on the left. I would take a screen shot of this, but the native screen shot app crashes every time it takes a picture, and the resulting .png is corrupt. The 22" renders as expected (correctly).
Once I move my mouse, the unity launcher reverts back to its correct position on the left. The desktop appears correctly centered, though it still renders the wallpaper image at 1680x1050 (movies, web videos, applications, etc all render in HD correctly at 1920x1080). If I enter "Displays" in system settings, everything appears correct, the monitors are lined up in expected order, the resolutions are correct, etc. When I enter "Appearance" in system settings, the desktop resolution states that it is 1680x1050. When I manually change the desktop wallpaper, it will change the resolution to the correct setting, and the wallpaper will fill the desktop size to 1980x1050.
I use a desktop rotation app (wally) and when it changes the desktop wallpaper, it immediately reverts to 1680x1050. There is no setting in the application to control this, and its set to fill the screen (it no longer does). Rebooting also reintroduces this problem.
I went into compiz display settings, and everything appeared as correct. I took it off of smart mode anyway, and forced the setting to prefer larger screen. No effect. I removed and reinstalled wally, also no effect. I played around with a number of dconf/gconf, compiz, and system settings, and nothing had an effect. It was as though I couldnt really control my desktop wallpaper display size in any way, and it was married to 1680x1050 instead of 1920x1050.
Just out of curiosity, I powered down and switched the DVI port for the 2nd monitor. Its now in the 2nd DVI port, and everything displays as expected. All settings are correct. Im baffled - why is it that I couldnt control this at the software level? Why does the DVI port matter beyond any reason other than positioning of the screens (which can be corrected in Display settings)?