I have a question
When I flashed the .srec file of a project or mpc5744p simulink example, the application starts only once and after resetting the kit, the application did not start. keep in mind that I flashed this file into the flash memory not into the RAM part.
Most probably your application is missing valid RCHW (reset configuration word).
Once you load program to micro via tool, it probably set IP (instruction pointer) to the start address. (Debuggers do this by default usually)
And once you reset micro, the device will start from BAM and in BAM it will look for RCHW which define your start of you application.
Please refer to reference manual: