Hi,
from personal experience I can say that it is definitely a software issue.
When you swap nozzles or pump heads, you need to adjust your pump voltage table to reflect these new hardware changes. Now, it would be simple if you could just proportionately scale your existing map and have it work - but you can't.
For this reason, most tuners leave the pump voltage stock and just do the "hammer" mod to set idle IQ, which alleviates the problem. However, since everyone seems to think 4-5mg/stroke is ideal no matter what nozzles, people are still having trouble. My tune, for example, was one of the ones you could not stop shuddering even with the hammer mod - after several revisions to the pump voltage table, the shudder is completely gone, response is ideal and much improved to before, ...
The thing is, when you're doing the hammer mod, it's like you're proportionately scaling - this will work inside pretty wide limits, because VW has set it up very forgivingly to take care of wildly differing climatic and other ambient conditions. However, once you get outside that "tolerable" range for the ECU, you start experiencing shudder - this is caused by the ECU not being able to correct enough. It'll go to max quantity correction and then swing back to low, then to max, then to low, ... -> shudder.
That's what regulation systems do if the error is higher than their "reach" to correct - they fluctuate wildly trying to regain control, though in vain.
So the real solution is to find a tuner that knows how to work out a pump voltage table...those seem rare! Also, since the amount of work involved is much much greater than just sticking a base tune on and doing the hammer mod, it'll not be cheap, probably.
Regards