On page 66 of BMI160 datasheet, it says that new data, orientation and flat interrupt cannot be latched. This means that the orientation interrupt always has a pulse with about 100us duration. If you read interrupt status register, then the orientation interrupt status bit will always be 0 because it clears itself so quickly. That is the reason why you can see the interrupt signal on INT1 pin, but you don't see the interrupt status bit to be "1".
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