Dear Iden,
I strongly advise you go through a book on Martix Analysis of structures( book by Weaver is good one) or go through a good text book on Finite Element Analysis ( By Bathe and Wilson). You have mentioned that you have checked using manual calculations by Finite Element method. To my knowledge you can't do a manual finite element analysis of a big system.Besides, how did you incorporate the bend flexibilities? You must be knowing how restraints are modelled in finite element analysis( typically by stiff springs)and how results change becuase of change in this stiffness value .Then there is the problem of "truncation error". Once these concepts are clear, you will understand why there is a difference between your calculation and Caesar output.

Regards