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What is the difference bettween debugging and running independently

Other Parts Discussed in Thread: TM4C129XNCZAD

I have a custom board with a TM4C129XNCZAD and using a Stellars ICDI Emulator.
I am writting the code interface to ET1100( an EtherCAT slave chip), it is in epi hb8 mode.
When I program and debug using the ICDI, the communication with ET1100 is ok.
When I quit the debugger and power the board down and back up, the TM4C129 running independently,  the communication is error.
I want to know What is the difference bettween two situation?
Thanks!