I have a somewhat similar problem. For me (Empathy 3.2.0 - Ubuntu 11.10, but it's been like this for a long time) the Messenger for Mac-users appears to be online, and they can talk to me without any problems, but they don't get my messages. When they send me a message, I can respond, and it appears to me as if the message was sent. However, they don't get anything at all.
I have a somewhat similar problem. For me (Empathy 3.2.0 - Ubuntu 11.10, but it's been like this for a long time) the Messenger for Mac-users appears to be online, and they can talk to me without any problems, but they don't get my messages. When they send me a message, I can respond, and it appears to me as if the message was sent. However, they don't get anything at all.