There are 2 aspects to the Reference Checking phase of the hiring process.
Like Syed mentioned, it's human nature to get unconsciously clouded when the same person is asked to corroborate/verify earlier findings....be it in hiring or just about anything else.
The only way is for someone NOT involved in the decision-making process of the hiring to handle the Reference Checks......to allow an open-minded facts-checking exercise.
In India, we have regular Background Checking/Verification Agencies that do reference checking also if needed......not sure about the scenario in USA.
The Second aspect is what Perri suggested.........I have faced similar situations where the References give a rosy picture [after all they are humans too], UNLESS asked pointed queries. Like the Saying goes: "If you want the right answer, you have to ask the right question".
But the minimum of queries that need explanations or long-winded answers the better, since explanations invariably tend to lead to masking the factual inputs needed to arrive @ a well-informed hiring decision......in a whole lot of chaff.