If the diaphragm is a 2-way deck, there is a critical difference in how the out-of-plane stiffness is treated (it's considered when the diaphragm is semi-rigid only in v14.7 and later). See RAM Frame Semirigid Diaphragms.
The other, more basic thing to check is the total base shear. If the total base shear is going up it could be an issue with the distribution of the load, wind loads on semi rigid diaphragms get applied to multiple windward and leeward edges, see: 
It could also be an issue with the building period which, in turn, affects the total shear.