You NEED to exclude outside light from your system. Thats why your "dark" reading is high as compared to this
I fixed this issue. Now the LED and the Phototransitor are inside a dark container that day light can not reach.
And I weld some wire to the LED and phototransistor to wire it to the breadboard.
Now the output is very stable:
ON: 989 OFF: 0 Subtraction: 989
ON: 989 OFF: 0 Subtraction: 989
ON: 989 OFF: 0 Subtraction: 989
The output from other phototransitor that is exposed to day light at the same time is:
ON: 973 OFF: 13
ON: 973 OFF: 13
ON: 973 OFF: 13