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The sensors in my build did not work correctly at first. I found that the black PLA (3D Solutech) I used was too transparent to infrared. I needed to reprint all the flags in black ABS. I first tried blackening the flags further with a magic marker. This caused the endstop's indicator LED to turn off, but the sensor still did not trigger. I wonder if your situation may be similar.
edit: Just measured the flag engagement of the endstop. The flag is engaging the endstop sensor by about 5mm.
edit again: The sensors in my build are BALITESEN sensors.