Hello,
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:

Best regards,
Peter