I am using SDK 14.0.0 with Softdevice S132 V5.0.0 and the accompanied DFU libraries. In the examples\dfu\bootloader_secure_ble example I think the logging system has a problem.
When compiling the debug version of this project using Keil MDK (pca10040_debug\arm5_no_packssecure_dfu_ble_s132_pca10040_debug.uvprojx) the output from RTT looks okay:

When compiling the same version with GCC, the output from RTT looks somewhat wrong:

The sources of the log output are wrong, as I do not believe that the clock is responsible for initializing the flash.