I'm guessing you subdivided while they were split, hence the gap? In the future you could try exporting, and then reimport it with a higher weld tolerance value.
This is awesome! Really think SD is the way of the future for textures! Love this tool and think the non-commercial license will help it find more users (who will love it)!
Aside from the few issues noted above, it seems to be working pretty well so far. Thanks for sharing, I'll definitely be putting this to use in the future.