Application doesn't work on S5D9 when flashed using J-Flash

Hello,

I have a synergy project for S5D9. using debugger J-Link application runs properly but when I flash the binary using J-Flash tool the application doesn't work.

Following are the configurations:

E2studio version: : 5.4.0.015

SSP version: 1.2.0.0 b-1

Synergy project with c and C++ files

Could you please guide me to resolve this isssue.

Thanks,