I also see this issue. I have about 8 current missions, each with their own alarm (maneuvers). At any given time I only see between 3 and 5 of them counting down. If I switch to the ship that is not counting down I see a different set not counting down (though the current ship always is one of the ones counting down).
There appears to be no relationship between the position of the craft and whether it ends up counting down. I suspect the order they were created might have a relation, as when I enter the tracking center it seems like the alarms created later seem to be the ones not counting down.
