Window indicators dont update properly

Steps to reproduce:

1) start Cairo Clock (make sure it is set to not show in the taskbar)
2) notice Docky doesn't show an icon for it
3) open Cairo Clock's prefs
4) toggle the show in taskbar pref
5) notice that Docky shows the indicator for 1 window
6) right click the item and you will see there are 2 windows listed, it should show 2 dots!

Similarly if you disable it, it will show 2 dots and not update to 1.

You can force an update several ways, such as focusing another window then focusing back on the clock.