The games task bar is out of our control. It will flash dependant on what is happening. For example: If I am alt tabbed when someone attacks me it will flash the task bar .. but it won't flash to tell me I have alt tabbed too long and gone AFK. It will flash if I receive a whisper but not if there is a guild chat.
So, maybe, if the addon gives you the option, turn on whisper mode so that it alerts you with a whisper. Just a thought. And if not available, you could either see if you can add that feature in yourself or ask the developers to.
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