I don't know the specifics of the production process used between JHA and the factory but I do know software development and if I've understood what has been reported here correctly, JHA use a "front end" software package to enter the values needed, (and understand that the data is much more complex than just 'up the treble a bit'; frequency, amplitude, time and possibly phase corrections are involved for each tweak). All through the early production JHA will be discovering and understanding new things all the time and I would guess the "core" code has had some tweaks by now. The code adjustments that tweak the code to each individual case and driver set also have to go through this translation process, again creating the potential for bugs to creep in.
The compiling software and the person who knows how to use it to compile this data into code the DSP chip can understand I believe is presently only at the factory in China and it's only too easy for errors to creep into the code translation process. As anyone who has worked in programming is aware, any little change to the source code can and often does create problems elsewhere in the software. That's why debugging software amendments is always needed, to find the new problems created in fixing the last one. Maybe JHA will be able to move the complete coding process in house one day, but they would need to be producing a hell of a lot of these things to justify the wages of a specialist like this.