Hi Martin,
Inspecting the code, it occurs to me that since the SYNCRDY interrupt wakes the processor, then PA14 (channel 1) should go low immediately after waking and then transition high 10 ms later. That doesn't appear to be what we see in the scope trace.
Moreover, the code indicates PA14 goes low when the MCU wakes from sleep. Thus, PA14 should be high when the SYNCRDY interrupt fires.
From the screen shot it looks like the scope is in "Auto" sweep mode. Could this be causing the visual artifacts? I've noticed in the past that "Auto" can sometimes cause confusing convolutions of signals because the scope combines multiple sweeps.
Steve