Hi,
I'm not absolutely sure, but is it possible you had a lot of sugars, adjuncts, extracts or other non-grain ingredients in the recipe? While working on BeerSmith 2.0 over the weekend I noticed that the program blindly totals all of the "fermentable" ingredients when scaling the mash profile rather than just the mashable grains. If you had a lot of sugars or other adjuncts this could be a problem. If this is the bug, I apologize. Surprisingly no one caught it in the last 5+ years or I would have corrected it much sooner.
If not, could you post the recipe so I can take a look at it?
Cheers,
Brad