I have been playing my Pontus II with the new FPGA firmware update for about a week now and I can confirm that the random pops/ticks I was experiencing are now absent. This mirrors my experience with upgrading the firmware on my Ares II. So it seems the issue was in fact software based. Below are the changes associated with the new firmware as described by Alvin at Vinshine:
1. The FPGA firmware update is for all DENAFRIPS DACs with the latest FPGA BGA chip.
2. It does not apply to the older DSP (Amanero, released in 2017-2019). If you have a DENAFRIPS DAC purchased after 2020, in general, it is upgradable.
3. The firmware update fixes some bugs, and enhance the sound quality for all digital inputs
4. The firmware update changes the NOS response to what Vinshine Audio believes it's NOS (Raw, Staircase Waveform output for 44.1kHz / 48kHz)
Areas of Improvement:
- Improved Adaptive FIFO Buffer & Reclocking Architecture
- Reduced the effect of Buffer overrun/underrun due to the Source's Clock and the DAC's Clock differences
- Reduced Audio Latency
- *Eliminate Phase Difference between L/R Channels
- Optimised DSP to improve the sonic performance"
I have to commend Vinshine for being very responsive to the issues I was having. Never did they claim this would fix my problem with certainty. I think their stepped approach to troubleshooting this issue was appropriate and worked out me in the end.
So if this was a software issue, why is the issue not being reported by more people? I don't have a good answer, but I tend to have very analytical tendencies. When I listen to music, I listen equally to my equipment. I would not be surprised if some Denafrips owners have the issue but haven't noticed because of the way they listen to music or perhaps to the type of music played.