I have the same problem with a Sig P226 Mk25
When I align the tops of the rear&front sights the front dot is higher than the rear dots. It is dead on with this sight picture otherwise (tops of the sights flush and the front dot covering the bullseye).
Unfortunately, when I align the center of the dots (night sights ***!!!!) it shoots 2 inches low at 7 yards, therefore, pretty much impossible to make use of the night sights....
I sent it to Sig Sauer just to be returned as is. They stated they failed to see the problem.
See the attached pictures.
conclusion: nice gun, not so nice price, terrible customer service
Never Again!