Something similar happened to me with SE RC1 if I remember correctly. I had to change the pixel value two times because the first time it didn't apply the values I entered, don't know if it's the same for you.
I forgot to consider whether you might be using an old version. I think that's your problem; that version isn't capable of making the window larger than your screen. You'll need to update to at least 0.9.7.3, or possibly the 0.9.7.4 beta.