The reason is inconsistency in statements, as per reports. And it is good enough reason to doubt a person and conduct further tests. Inconsistency, in statements of parents can be expected even, if they are innocent, and will not a major ground for further inquiry. But they aren't expected from Krishna and thus raise doubts on his integrity and further probe is expected.
Just because parents are rich and have good contacts does not mean that they have to be the culprits. Given the situation, nobody can be pinpointed. So, at least let further evidence come up before making a decision on fairness of the investigation. At least CBI is coming up with scientific reports to back up their claim.
