So I just got off a call with Apple Customer Support and realized Scaler 2.5 was the issue:
Essentially, if I have Scaler loaded as a MIDI FX on an instrument, and create (or duplicate) the track to load another instrument with a different instance of Scaler, when I have the new track selected it will play as normal, but if I then select the old track, it will continue to trigger sound from the new track only (and not play the current instrument selected). Then randomly no sound will come out of either instrument while selected. This essential makes it impossible to do anything with Scaler. Also Logic has been crashing randomly whenever I am using Scaler but without it is fine. Please help and fix this bug ASAP!