This appears to be related to window matching, the icon we see for tomboy in the launcher is actually for the "Search" dialog, not tomboy. If you close that window, the launcher goes away and doesn't show the arrow saying it is running even though it still appears in the indicator with the menu.
Somehow we need to special case this so the icon can match tomboy not the search dialog, I assume.
This appears to be related to window matching, the icon we see for tomboy in the launcher is actually for the "Search" dialog, not tomboy. If you close that window, the launcher goes away and doesn't show the arrow saying it is running even though it still appears in the indicator with the menu.
Somehow we need to special case this so the icon can match tomboy not the search dialog, I assume.