Comment 3 for bug 1315041

Also occurs for me. The indicator seems to only update when the application loses focus instead of when the current window loses focus (which would catch every case except if an application opened a window in the background). So alt-tabbing to another application will fix the window markers.

Open Terminal
Open Chromium
New window. (I now have two chromium windows open but only see one marker.)
Switch to Terminal. (Chromium now correctly shows two window marker.)
Switch to Chromium.
Close window. (Ubuntu switches to terminal since it is the last window active. Chromium correctly shows one window marker.)