My experience agrees with "Flange Side Doesn't Matter Brown".

That said, whenever I lace up a wheel onto a new hub I always do it with the trailing spokes on both sides coming from the inside of the flange. I've always done it that way so it's a LOT faster for me to do it that way. I laughed at how much trouble I had the last time that I tried to relace an old hub that had previously been built the other way around.