Factory double glazing features a sealed void between the panes of glass. Air is drawn out, creating a vacuum. An inert gas such as argon is then pumped into the void.
DIY double glazing can be very effective, but there will always be air in the gap.
I'm afraid I can't think of any way to overcome this. I guess it'll always be a case of removing the secondary occasionally to clean up.
I guess a small pack of hygroscopic crystals would soak up some of the moisture, but it would have to be replaced fairly frequently.