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After you charged the batteries back up and connected to them to the truck while everything was off, was there a spark? There isn't supposed to be any load without anything on. I've had my s3 box fry a relay which left the glow plugs on and killed the batteries really quick.

yep, if it says smart start then its newer. You can also tell because they have the small testing port on the front.

You could always take the box out and take it apart and see whats blown. If fixable it will probably cost less than a new S3 box.

That S3 box is the latest and greatest version. Sounds like you fried your box though.