in 2.6.0 Beta 2 there was a bug, that after selecting "Alert when available" in the context menu of some away/offline/dnd contact one were getting a popup with any last message sent or received, so it wasnt related to that contact becoming available
now in the current SVN version i see that it only starts to flash a taskbar and no popup is shown. I think popup in this case (as the common message popups) is very useful. I think such popup could be showing "User is online" so one would know what is going on without having to click on that flashing taskbar window. Especially when "Notify when a user comes online" is disabled. Personally i have disabled that, as i dont need to see bunch of such popups constantly in my ~200 users roster, but i do want to get a popup when i select "Alert when available" on some contact.