Closing this bug as it seems that it was solved by itself. Feel free to
remark the status as "New" if this is still an issue.
** Changed in: empathy (Ubuntu)
Status: New => Invalid
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After a reboot, the conversation windows start to pop up correctly.
Weird.
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https://bugs.launchpad.net/bugs/1168371
Title:
incoming messages not opened in a window
T