This has happened to me on both the 12.04 installs I have tried.
Sometimes, maybe 3 times a day, when I switch workspaces to go to programs I leave open in other workspaces, the Window isn't there. I find them in odd positions - for example, I just found my browser window half off the bottom of workspace 4, wrapped around to partly in the top of workspace 1.
What makes it more likely to happen appears to be when a window has a child window/dialog open. The child is very likely to be displaced randomly?
Edit: have switched off all extra workspaces - now just working in one, because I got tired of hunting down lost app windows. Either no-one else is seeing this, or else no-one has any solution.