When running in stand alone mode without the debugger, the .cfg file is not executed on the target board.
I suggest creating a stationery project for your 52223 evaluation board for an example of board initialization. The stationery project has the minimal setup and code to get your evaluation board up and running.
In this stationery project for the internal flash target of the project please pay special attention to the MCF52223_sysinit.s file. In this file there is the _asm_startmeup section that is the main entry point upon hard reset. The memory map is setup based on linker file definitions and then the higher level system initialization routine is called. After that it jumps to main. Then in the M52223EVB_sysinit.c file there is the SYSTEM_SysInit routine. Out of reset, the low-level assembly code calls this routine to initialize the MCF52223 modules for the M522223EVB board. So these would be the places to add your board initialization sequence.
I hope this helps.