It sounds to me like your efficiency numbers are off. If you are getting the correct pre-boil volume, then you need to measure your pre-boil gravity and compare that to the beersmith calculated pre-boil gravity, and adjust your efficiency number till the system calculates the same pre-boil as...
Here is a complete step by step, how to do it, taken from a link on the Stout kettles and tanks website
http://conical-fermenter.com/info-discussions/build-your-own-automated-fermenter-chillerheater-for-200/
I am sure they will make good on it. Dissappointing to be excited about getting a new piece of equipment and then not be able to use it. Let us know what they say.