I've finally worked around some funky bugs that only appeared after updating to 15.3. In my app, I had to change my clock source to RC or SYNTH to make it work (was hanging on enabling the softdevice). My XTAL setting worked fine in 15.2. When I got to working with DFU, I had some issues and tried everything mentioned on here (mergehex to fix the UICR/MBR bug, fixing the Makefile, etc.), but still couldn't get the DFUTarg device to appear. Loaded the debug version of the DFU module and stepped through it to find it failed to execute past the command to start the softdevice. It dawned on that this was probably the same issue that prevented my app from executing. After changing the clock source, everything worked as expected.
Now my question: What changed that makes the XTAL clock setting work fine in 15.2, but not 15.3? I'm using the DVK-BL652-SA device from Laird. Is there any issue using the SYNTH clock setting if power consumption isn't really a concern?