I wasn't quite sure if you were saying that the problem is that the new track always goes to a default setup in podfarm, or if you were saying that after you change the amps etc., the sound stays nearly clean.
I have never done this before, but I have just tried to see if there is a way to copy the exact setup and then put it on a new track, without going into podfarm and scrolling down to the saved setting. I discovered there is
In my programme (not cubase) I right click on pod farm's thing on the track and select clipboard and 'copy effect' and then I go to the new track and right click and clipboard and then 'insert effect track', and it places pod farm onto the track and with the saved amp/effects from the other track.
I don't know how this is done in cubase, but if this is what the problem was, have a look in cubase for clipboard and copying effects etc.
If you were meaning that it for some reason is not changing the sound, then it may be that somehow something is changing things in podfarm. One thing to check is that one might have the gate on in the top left and one not.
If I misunderstood, your question has at least helped me find a quick way of duplicating tones, so thanks
Let me know if I have misunderstood the question and if anything has helped at all,
Is it possible when you copy the PodFarm settings onto the new track, the plugin is inactive? I have seen that happen in Reaper, and need to check the box that makes the plugin active.
OR - you are not monitoring the new channel that has been created, just monitoring the input.