Unity in 12.10 comes up behind other windows

TL;DR: disable and re-enable unity plugin in CCSM.

Walkthrough

• (optional) if you have compiz config setting manager then issue

  apt-get update && apt-get install compizconfig-settings-manager

• Launch ccsm (either on command line or through dash)

• Then use the search box and type "unity"

• click on the plugin
• on the left part you can uncheck box to disable unity
• re-enable unity by re-checking the box.

Note: This answer was in a comment of the lengthy unrelated accepted answer.

Note2: This answer works for the current session but won't fix definitively the issue

I believe I have found an answer myself. I'm not sure exactly what solved it, so I'm going to list what I tried and didn't appear to work also.

First, I tried the fglrx driver. I installed this using the tab in "Software Sources". When I rebooted, the first thing I noticed was that the Ubuntu splash screen only came up on two of my three monitors. Then the login screen came up similarly on only two monitors. Interestingly, the montors were not "mirrored", as with the xserver-xorg-video-ati driver, but only one screen had the login prompt, and the others just Ubuntu logos.

Having logged in I tried all sorts of ways of configuring the display using both the Ubuntu display controls, and the ATI Catalyst Control Centre, but no amount of fiddling could get all three monitors working. It kept claiming that either the monitor wouldn't come on, or that there wasn't enough memory, despite the fact I've been using it triple-head for years.

On the plus side, the 3D effects did seem much snappier, and the Unity dash and HUD did come up on top. Some might consider this a fix, but I was still one monitor down.

Second, I tried the fglrx-updates driver, also selected in "Software Sources". I observed no apparent differences to the straight fglrx driver.

Finially, I restored the xserver-xorg-video-ati driver, and tried playing around with the Compiz Control Centre (actually, I'd tried this before, but failed to fix anything).

After much futzing with Compiz Plugins that didn't fix the problem, I eventually disabled the Unity Compiz Plugin. This made all the Unity UI elements vanish. For a while I thought I'd stitched myself up because none of the windows would respond, but then they came back to life, another application-switcher got enabled, although there was still no obvious way to launch new apps. I then re-enabled the Unity Plugin, and everything came back the way it had been, but with the Dash in front of the other windows where before it had been behind.

So far, fingers crossed, the problem has not recurred, so I'm considering it solved. :)