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Examples built with GCC do not work, prebuilt hex files do work but only if programmed with nRFgo Studio. Any idea why?

I'm new to the nRF51822. I've setup GCC and Make on Windows 10 and am using SDK 11. In all the examples of the SDK, flashing the newly made hex files (using GCC) with JLink, nRFgo or nrfjprog doesn't work. Even after flashing the softdevice i.e. The programming happens successfully, but the nRF51822 doesn't advertise or carry out any of the instructions.

However, if I flash the nRF51822 with nRFgo, as an application with the prebuilt hex files included in the SDK under example_name\hex, it does work. Advertising, etc.

Any idea how I can solve this issue?

P.S. The files compile successfully. So I think I've setup everything correctly.