Dan,
The losses (trub, chiller, etc) are only factored into the water calculations and do NOT affect the predicted OG.
The reason for this is that the standard method for predicting OG is to use only the "theoretical" OG times the overall brewhouse efficiency. This means that to account for large trub or chiller losses you need to lower your overall brewhouse efficiency.
This may seem a bit counterintuitive, but if I went with another method such as actually calculating the effects of each system loss then BeerSmith would not be compatible with the other programs and formulas commonly used in brewing.
I have considered a modification that might "optionally" allow the user to enter their "mash efficiency" instead of brewhouse efficiency and then perform the loss calculations from that point. This is a possibility for a future release, but I have not yet implemented it.
Cheers!
Brad