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How is it that our instant tests that read positive are sometimes received back from the MRO as negative?

That is exactly why the lab confirmation test is necessary.  The instant test is not accurate for negative positive results.  It could have been an over the counter medication, it may have been reversed by MRO due to a prescription or perhaps it screened positive but did not confirm positive.

That is also why we never say the instant test is positive, if it is not negative – it is always inconclusive until confirmed at the lab