Hey Shane,
Your description is a bit confusing. I am getting notifications. I do not get
notifications if the chat window is opened.
Is that the bug you're describing?
Is it something like this one?
https://bugs.launchpad.net/ubuntu/+source/empathy/+bug/400352
** Changed in: empathy (Ubuntu)
** Changed in: empathy (Ubuntu)
Status: Incomplete => Invalid
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Empathy doesn't notify in the same way as pidgin (Karmic)
https://bugs.launchpad.net/bugs/392935
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