I tried this in Cakewalk by Bandlab but it should also work in SONAR X3 Studio.
In the [Options] section of your TTSSEQ.INI file add the following line. This prevents the first Patch/Bank event contained in a MIDI file from being moved to the track properties when you open the file.
GeneralMidiSMFs = 0
As I have Cakewalk By Bandlab, I am not sure where this file is for SONAR X3 Studio.
I am thinking somewhere here somewhere (or something like that):
%APPDATA%\cakewalk\SONAR X3 STUDIO
Note: You really should consider moving to Cakewalk by Bandlab. It free and light years ahead of SONAR X3 Studio