I select links in Thunderbird that normally opens Firefox to display the linked page. However, after a time using the environment, Thunderbird will call the link and open a tab for it in Firefox, but Firefox will not come forward. It just stays in the background. It will act correctly if closed and the restarted. It is only a guess that this function is controlled by Exo, and that the environment loses control of the app connection.
I am using Fedora 18.
This may be related to exo or the window manager that you are using. Does this still seem to affect you with Xfce 4.12?
While I have seen this problem in various configurations, this post is quite old and no longer applicable due to the various upgrades and changes since the original date.