virtualbox.org

I have been running Ubuntu 11.10 guest under windows 7 with virtualbox 4.1.14 with no problems. Yesterday, I upgraded to Ubuntu 12.10, re-installed the guest addtions, and now it mostly works, however in seamless mode, it still shows the Ubuntu background, and I can no longer see any Windows 7 windows that are still open the way it used to... so it's not really seamless anymore, it's just a full srceen that still has my windows task bar at the bottom. Seamless mode with all my other operating systems makes the background clear so you can still see and interact with other windows on the host system. I do not have this problem with any other guest OS, and my backup copy of Ubuntu 11.10 still works correctly.

Unity 3D or 2D?
3D with compiz is a known issue (see your VBox users manual) that has never been resolved AFAIK.

how can I find out if it is 2d or 3d? It is the standard ubuntu install with no modifications, and I just did an upgrade to 12.10, and that is when it stopped working.

You change from Unity 3D to 2D at the Ubuntu login screen. You listed 12.04 at the start so hopefully this is just a typo.
Ubuntu 12.10 is pre-alpha and really not supported yet.

oops.. it was a typo, I have 12.04

I loged off and loged back in selecting 'ubuntu 2d' and its doing the same thing. I only had options for 'ubuntu' or 'ubuntu 2d' nothing about unity.

To see what flavor of unity. Type ps -ef | grep unity

You should see something like I have below.
jpowell 1425 1223 0 12:22 ? 00:00:00 unity-2d-panel
jpowell 1426 1223 0 12:22 ? 00:00:11 unity-2d-shell

I can confirm that seamless mode does not go to a transparent desktop on osx 10.8.2 MacbookPro retina. I tried with my Ubuntu 12.04 and WinXP virtual machines. Both have all the most current guest additions.