Short Answer: It is not Node, file is really changed twice.
Long Answer
I have a very similar approach that I use for my development setup. My manager process watches all js source files if it is a development machine and restart childs on the cluster.
I had not paid any attention to this since it was just development setup; but after I read your question, I gave it a look and realized that I have the same behavior.
I edit files on my local computer and my editor updates them over sftp whenever I save. At every save, change event on the file is triggered twice.
I had checked listeners('change') for the FSWatcher object that is returned by fs.watch call; but it shows my event handler only once.
Then I did the test I should have done first: "touch file.js" on server and it triggered only once. So, for me, it was not Node; but file was really changed twice. When file is opened for writing (instead of appending), it probably triggers a change since it empties the content. Then when new content is written, it triggers the event for a second time.
This does not cause any problem for me; but if you want to prevent it, you can make an odd-even control in your event handler function by keeping the call numbers for each file and do whatever you do only on even-indexed calls.