Okay, I have no idea what this was still but I fixed it.
Basically I went in and assigned the master output level, right click the output knob in TH3, to an empty automation slot. Then I went into the instruments automation panel and pulled the line to 100%. This doesn't change the output level, however, what it does do is make sure that it will not change of its own accord again and you can set it yourself freely.
Celestial Borhau's post in TH-3 Locks Output Level (FIXED, SORT OF) was marked as the answer