Shreddage Hydra - Playing Higher Notes Louder in Chords?

[EeveeonE]

I don't know why this has become an issue, but it has.
I can't attach the video for some reason. It's an MP4.
To describe the issue, I'm playing a (I'm not too familiar with chords, bare with me) F#3, as palm mutes, and there's two every beat in a 4/4 time signature at 225 BPM. Problem is, the higher notes are more visible than the lower notes. I'm using STL Tonehub over it, which shouldn't be an issue. The treble and mid were high, I turned them down, but got the same issue. But it just makes the chords sound awful. I'm not sure how do fix this because it's something to do with Shreddage.