Ive had the same issue with both Materia Extraction and Turnins of Collectables.
What i came up with is this:
//extract
key(< ,1.5)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
Key(num4 ,0.2)
key(num0 ,0.2)
Key(num4 ,0.2)
key(num0 ,4)
key(< ,1)
< is my key to open the Extract window, 4 is left, 0 confirm.
As you can see ive included a 4 before every extraction. That usually activates the window so the next inputs go through. And if the window is already open a 4 wont mess anything up.
This is 6 extracts which usually takes 10-15 ingame minutes (et). You can add more blocks but i usually like to run more smaller extractions instead of less bigger ones.