The structures containing the scenes to be added for that frame were implemented as sets, which meant they were ordered based on the string name of the scene. This meant that multiple calls to this function would not add the scenes in the order they were added using logic.addScene(). I have implemented these structures as queues, which gives the desired behavior.
Original bug [#32218]: http://projects.blender.org/tracker/index.php?func=detail&aid=32218&group_id=9&atid=306
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Any reason to use a queue instead of a vector? Seeing as vector is already included, I'd be tempted to use that.