Maybe someone mixed up the spacers? I imagine there should be a similar amount of spacers on either size.
You can fix that pretty easily. Move spacers around (thinner locknut on one side etc.) so that you get good chainline both ways. Then redish as necessary. (Edit: You sure you have a similar cog on either side?)

BTW, I would just put the damn wheel in the frame to see where the rim has to be... dish it so that it ends up in the middle of the frame. Or get/make a dishing tool. The position of the hub is totally irrelevant (apart from the fact that you should dial in the hub position on the axle before you go about dishing)