Concerning Ubuntu 12.04 with either Unity or Classic Desktop
I find that certain apps, so far noted, the home folder (nautilus) and the Text editor (gedit), will open behind the already open apps on the screen.
Most apps on the Unity bar open out in front.
I just selected the Classic Desktop, and the Places menu > Home opens up behind the already-open Firefox. Same behavior as found in Unity.
I can open Files from the applications menu and arrive at the same behavior, it opens the Home folder behind Firefox.
I had already opened the Home folder, and now I find gedit will open off the Applications menu out in front, as it should. The second opening of Home folder opens out in front, as it should, after I've closed it, at least here in Classic.
I suggest repeating this experiment from a fresh boot, open an app, then open either of Home or gedit.
My most usual apps to open are Thunderbird, or Firefox, then gedit or Home.
From the Classic Desktop with no animations, I have so far found Home will still open from behind. Gedit opened out in front its first time, but I need to start from scratch and see if gedit will open out in front of something else as it should, or opens in behind as has been my experience with Unity, if it is the second overall app to be opened.
My expectation is for every app newly-opened will be placed out in front of anything else that's been opened. If it was a mistake to open it, I can close it, but usually I want to USE it.
I cannot copy from an email in Thunderbird and paste directly into an edit form on a web page in Firefox. I need to first paste it into a text editor to clean up any unseen rubbish picked up in the copy of the plain words in the email, THEN copy from the text editor and paste into Firefox.
it burns me every time when my text editor plays hide-and-seek behind the open apps on the Desktop.
Example 2: I have some standard boilerplate that I saved to a text file and I need to navigate the file system to find the file, double-click it to open, and copy from the test editor to paste it into an email or into a web form. The file system opens up behind everything and plays hide-and-seek with me when I am trying to get something done.
Than you, whomever takes on the effort to sort this issue out.