your question is very much clear and i will try to explain my opinion.
There is a difference in determinate and indeterminate structures, i.e. the statically determinate structure will only resist in couple action, but indeterminate structure has a number of alternate ways to resist the applied...
another point is, that for each material, moment transfer is different. for steel, we can assume a fixed joint for a complete transfer of moment. but still we dont introduce fixed joints. in rcc we assume rigid connections transferring full moment at joints. due to complete or partiall transfer...
Almost all softwares use different values of EI for different materials. e.g. u can find defining material in stadd pro, etabs, sap2000, etc. if you define the material as concrete, steel, timber etc you will find different values of EI as default values. And also we can modify the values...
which load cases did you introduce? have you checked the moments against each load case? or only against 1.2D+1.6L Factored ?
It also depends whether you are iterating with P-Delta for seismic lateral forces or just P-Delta effects due to sidesway, wind lateral or lateral deflection effects. It...