I'm seeing some flaky keyboard focus issues with IntelliJ IDEA. I've got IDEA 10.5.2, and am running OS 10.6.8.
The problem most often occurs when I'm using the version control diff window. Once the window is up, I use keyboard shortcuts to navigate: control-left/right to switch between changed files, F7 or shift-F7 to navigate diffs.
What happens is that sometimes, either just after the window opens, or just after I use control-left/right to switch files, the diff window loses focus. The window appears to have focus but any keystrokes go to the main window instead. It usually takes a few seconds before I realize it, but it's apparent when I go back to the main window and my editor tabs are all different! Or all closed; if I hit command-F4 to close the diff window it ends up closing the frontmost open editor buffer.
I've found that I can use command-~ to switch from the main window back to the diff window to fix the keyboard focus issue, but this is an annoying workaround.
My guess is the issue is caused by the window I occasionally see that comes up when switching between files -- a progress window that's only visible for a second or so, presumably while intellij is waiting for data from my sccs (subversion).