Beer smith takes into calculation boil duration IBU extraction efficiency, I do not use brew pal so I do not know about them. IBU Extraction Efficiency – they longer you boil the more Bittering units you pull from the hops. A 60 minute boil does not mean a 100% extraction; at most it would be around 35%. Some think if you boil longer you will extract more – hence 90min boils on IPA’s, - I disagree with this as do other people, but some people will have a difference of opinion. I have tried and tasted and the difference I notice with longer boils on the same recipes is higher Alcohol content. I do not notice a dramatic increase of the Bitterness of the beer. (But again I don’t send my beer in to be tested so I can only go by my taste comparison/ I have no scientific proof) So this may be why they have different results the efficiency may be set different (or as previous post the Alpha Acids may be listed different)- I know that you can adjust beer smiths AA by editing the ingredient. In the end I do use and like beer smith, but I also use beer alchemy and I am still comparing both of them, I think I am starting to like alchemy better. (Only reason for this is personal preference, I like the print out of Alchemy for my recipes and batches so I can put them nicely in my brew binder.)