Are you using BS2 or BS3? In BS2, acid malt, acids, and water salts added directly to the recipe were not included in the pH calculation. For BS3, this was changed.
Note also that the pH model being used in BeerSmith was developed by Mark Riffe and he recently came out on HBT stating that his model overestimates the buffering capacity contribution of the malt. This basically results in the model estimating an acid or acid malt contribution about 60% higher than it really needs to be. Reversing that, it underestimates the acidifying contribution of those materials by the same factor. Edit your acid malt to increase the acid content to about 3% to 3.2% (from the 2% as specified by Weyermann).
Next, 2 kg of acid malt in what grain bill? If I added 2 kg of acidulated malt to my 2.5 to 3 kg average grist bill it would certainly have a large impact. Conversely, If I were brewing 10 HL, it might hardly make a budge in the pH.