I am very familiar with the issue, and it ultimately caused me to sell my Pontus II. I now use an admittedly much more expensive Aqua La Scala DAC, but would likely have continued with the Pontus were it not for that issue and the way that it has been handled by Denafrips.
This has now been a known issue for at least a couple of years, and no, as far as I know, there is no software/firmware fix. So I believe that the company made a calculated decision to engage in damage control, rather than offering a hardware fix, which would have been expensive, assuming that they have the knowledge to execute such a fix.
There was also what I consider to be an effort to obfuscate, or deflect blame, by floating the suggestion that it was only happening with certain transports. I had the issue with a Moon 260DT, which is a high-class machine, and in any case, the Pontus is responsible for the problem, as it should obviously work smoothly with all transports.