Yeah no problem. You should select program controls LED if you want it to. This way you will also get colored LED depending on how you did assign colors (assuming you downloaded from the link posted one reply above).
You can run the LED test if you suspect an LED is hanging. Oh also the mark calls as read will not work on the 8100 as it handles messages differently.
The LED that was flashing was the BlackBerry OS (since you still have an unread phone call in your folder).