The Subterranea is designed to take whatever you put into it and synthesize a note from it. It has some filtering and tricky logic built in to the tracking portion which is trying its best to filter out what you don't want and only track what you do want, but bass and guitar signals are all over the place and analog computation in a small box can only be so clever. The envelope of your input signal is also tracked and then superimposed onto the synthesized voices. This enveloping was designed to be more dynamically-sensitive than if it were a more typical hard gated arrangement, which is important since the Subt was mainly intended as a front-end for filters like the Xerograph Deluxe. If the Subt created flat on/off dynamics then it would not interface well with an envelope filter and you'd just get two filter frequencies instead of a smooth sweep across a range.
Anything you can do to remove noise, especially high frequency noise, before the Subt will make the tracking much more solid. Rolling off treble at the bass is a good start if possible in your application. Generally if your pickups are weak then the dynamic range between your signal and the noise floor will be smaller, so it would make sense for this to affect the tracking. Compression can help or hurt depending on the comp, since some will end up boosting noise when you stop playing, while others have a non-flat frequency response which could help enhance the frequency range you're trying to track.
I would definitely like for this pedal to track perfectly for every player with every instrument, playing with a light touch or a heavy hand, but the Subt as it is represents the best Don Stavely (co-designer) and I could get it across a variety of input signals while keeping it fully analog. If a Subterranea 2 ever were to come out and improve on this (no such plans at this time), tracking any kind of signal perfectly, it would either have to have some considerable digital stuff going on, or there would be several trimpots inside that each user will need to tweak to match it to their instrument. My experience with the latter, on the first IE pedal (Cygnet tremolo) was that it caused a lot of confusion and annoyance for customers and overall probably meant that most people who had one did not have it set up properly and so ultimately performance was worse than if they weren't there at all.
So, removing noise, rolling off treble, and experimenting with boosting or lowering the input signal level should help find the spot where it tracks best for you. If you have a compressor with some tone control options that's a good companion as well. If you're not able to get it working the way you'd like, I do of course accept returns as I wouldn't ever want anybody to feel stuck with an IE pedal that's not working in their setup.
but a lot of people said to use one to improve tracking, so I assumed it might help for this issue as well - sorry if I said something stoopid!
