At 12.04, dual monitors worked perfectly. After upgrading to 12.10, the primary monitor works, the second monitor only partly works. I am sure there is some difference between the releases that I have missed setting properly. System settings -> Displays show both correctly as Acer 22" monitors at 1680x1050 (16:10).
An icon on monitor 2 is present, but elongated; almost an artifact, since other icons on the primary screen are absent, but this one icon is there on th second monitor. Selecting the icons on both screens exist. Painting is weird on monitor 2. Launcher exists and works on both screens, but even with sticky edges off, the cursor stops at the left edge of monitor 2. Clicking on text editor on screen 2 launcer will launch gedit there. If I drag it, it leaves a trail of after images like repaint is failing. If I drive the cursor on the launcher, the help tags like "LibreOffice Writer" appear, but stay on screen unless I drag the active gedit window over them. Then part of the help bubbles are overwritten, leaving behind after images of the gedit window on screen.
What is really fascinating is that the System settings -> Displays is now ignoring monitor selection, after allowing it earlier. Just before this, the help popup which said "Select a monitor to change its properties; drag to rearrange its placement" actually let me do that.
Maybe a trick of where I grab the edge of the monitor in the Displays setting. I just found a working handle. When I drag monitor 1 to the right of monitor 2, "Apply" and confirm, both monitors work normally (although the right monitor lets the cursor slide off the right edge onto the left edge of monitor 1 - which sounds correct). Painting of windows does not leave an after image.
However, success is only temporary. The setting survives the reboot, but painting on the left monitor, now monitor 2, now replicates the issues from before. The after image of the gedit window and the small window for "Are you sure you want to close all programs and restart the computer?" are still on monitor 2 (on the left now), even though they are not real windows, nor do they have processes behind them.
Curiously, in Displays, the "green" monitor on the left in the display window is matched by the right monitor color in the monitor upper left corner. Probably makes sense as the one on the right is now monitor 1. If I repeat the "drag the left monitor to the right of the right monitor on the "Displays" window, things are oriented properly, with no display artifacts as I drag windows around either screen. Also the description bubbles that pop up are overwritten on both screens, so none of those artifacts either. This goodness does not survive a reboot, however. Have not tried logging out and back in. All of this after positing that the motherboard VGA and HDMI ports could have been the issue.
So, I installed an e-GeForce 7600 GT Dual DVI (I know the web thinks it is not DVI, but VGA, but the connectors are DVI). No change to the weird behavior. The good parts continue to work, the weirdness also works, and swapping monitor positions seems to cure the issue.
So, is there a setting I have missed? Given "swapping" monitor 1 and 2 on the System Settings... -> Displays makes it work, just not across boot, I suspect so.