I've noticed this behavior in Lion's Terminal.app:
Let's say I have some text selected in a non-active terminal window. Meaning, another window is active – it could be another terminal window, or another app's window. If I click on the window with the selected text without clicking the selection itself, the text remains selected when the window is activated. However, if the click happens to be on the selected text, the text becomes unselected.
Is there a way to prevent the unselect behavior? I have to consciously avoid clicking the selection, otherwise I need to re-select (very annoying because text-selection often requires precise pointer movement).
The behavior is also inconsistent for no apparent reason – why have special behavior if the text is clicked?
UPDATE
This only seems to happen with the Basic profile (I haven't tested all of them though). If I use something like Grass or Homebrew, the selection is retained.
Best Answer
If you're perturbed every time you move the mouse (like me), you could alway try switching to keystrokes.
For example, to switch between open applications, use CMD+Tab, and then between windows using CMD+~
Another useful way to get around with the keyboard is to use Tab to move between all controls using the Keyboard control panel in System Preferences like so: