First three things I would check out:
1. Attic. Maybe the running sound is actually above you and somebody(or an animal) likes running through your attic.
2. Pipes. It could be a noisy pipe under the floor with air trapped in it, possibly hitting against the floor itself.
3. The Dog. Can you be sure that the dog is downstairs, and not running into your room then hiding under the bed or something? It might be a rat doing the same thing too.
Of course your comment about the door shutting goes against all this, unless your door moves around from any slight vibration. Also I don't see these things are emulating the sound of running human footsteps very well, but you never know how your mind might play tricks on you at night when you are scared. As for the perfume, I have no idea.
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