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I had a hard time with this one too, but the way I did it was naming my files in the correct order.  What I did was name each file in this format - <name>.SE01.EP01.ext.  I named my first file Firefly.SE01.EP01-EP01.mkv (I had to name it like this for some reason so the rest of the files would add in the correct order as they were not at first - the first file was a two parter for the Serenity episode, but naming it just EP01 screwed it up, so I had to put EP01-EP01, not sure why this worked), then Firefly.SE01.EP02.mkv, and so on.