There is some degree of monitoring active, creating a feedback loop - the interaction between the direct signal and the monitored signal creates the peaks and dips in the response. Need to track down and disable the monitoring (or set its level to zero).
Thank you John. I contacted Apogee support and they made me reset the Quartet. Now I get a flat response for loopback. I am looking to recreate the issue to get a better understanding on what was happening. Your explanation seems to fit the bill; low frequencies in phase adding and mid to highs out of phase creating the sine wave response.
Will check to see what monitoring I had set. The reset possibly switched it off. Thank you for your reply.