When I'm in dual monitor mode (not mirrored mode; mirrored mode works 100% fine), the applications are stretched, and my mouse clicks don't line up with the applications. See the attached image. Notice the highlighted text in the webpage near the middle of the two screens. My mouse was where the red dot was when I made that highlight. (The mouse doesn't show up in screenshots I guess.)
I was supposed to have the application menu bar on both screens, but it and the menus only show up on the right screen. They work fine relatively, though sometimes as dropdown menus close they momentarily visibly stretch like the applications are.
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System information:
I was running Ubuntu 14.04 with the nvidia-331 drivers, dual monitor mode was working great, but then in the last few weeks it started acting up like this often. Probably related to some recent updates I guess. Logging out and back in would sometimes fix it. I decided to do a full reinstall to 14.10, but now the issue always happens.
The login screen and gnome-shell both work fine with dual monitor mode. (I'll boot up my computer, see the login screen on my left monitor with the background going to the right monitor exactly as it should, I'll log in with Unity selected, and then it suddenly decides to stretch everything ridiculously until I switch to single or mirrored monitor mode.)
I do not get this specific issue when I use the default nouvea driver, but I do get tons of graphical artifacting and the screen freezes eventually when I'm in dual or mirrored monitor mode (single works fine), so that's not an option for me.
I'm currently using the nvidia-331 version 331.113-0ubuntu0.1 package. I've tried downgrading to nvidia-331 version 331.89-0ubuntu5, and adding the xorg-edgers PPA and upgrading to nvidia-346, but the exact issue persisted.
nvidia-331 are causing a lot of issues. There are some some fixes scheduled in the next weeks.