Playing in ATM9-Sky, unable to use my middle mouse button to set a custom amount with the threshold export bus. I can increment the amount by left/middle clicking with a stack of items, and decrement using right click too.

it is a keybind issue. inventory tweaker's item sort also uses middle click so it won't work for ae's. you can set its keynbind to other hotkey or just unbind it.

I see what my problem was, you are using the default keybind of minecraft to pick up items, I removed this so this was no longer working...

I see this is also the case for the AE2 lol, maybe better to use another option to take this key event?

The issue still remains even when removing the keybing, I removed every related middle click keybing and still does not work, also there's no option to configure another key to change those values

i think you shouldn't change vanilla mc keybind at most time. maybe in future i will add an another keybind for this action