ELF download behaves differently than initialized hex

Are you using printf for debug or do you have any other data output on the jtag uart port?

Please note that if your bsp is configured for reduced drivers, there's no control on the jtag connection. So, the involved code gets stuck if you keep on sending data and you don't have the jtag interface attached. Since usually the printf calls are located in main(), the final behaviour is the same you observed: the program flow seems to hang, but isr are still active.