Hi Kursad,
I will suggest also check all the calculations which are dependent on PWM frequency such as PWM duty cycle etc.
From waveform, it looks like when speed is ramping up to 14-Bits value (16383) then your Motor is out of control, means it’s running with maximum RPM (lost control), so there is chances that any of the control parameters is going out of range or overflowing.
And if motor is not drawing high current or device is not heating up then I think it should not be dead time issue.
Thanks
Abhishek