It sound like you mean polarity. Some speakers interaction with the room correction software will do this from time to time. If you know the polarity is correct, just ignore it since it will not result in speaker damage. This is common on some Pioneer avr's. I don't use Audysee, so I don't know if it will complete the autocalibration under those conditions.
Klipsch RF 7 based HT 7.4, Pioneer SC 35, Acurus 200 Five, Dayton 18 Ultimxa Dual Sub Cab(2), Dayton 18 Ultimax Large Vented Sub Cab (2), on Berhinger I Nuke DPS amps, Samsung BDP F 7500, Asus/My Book Live HPC 4 TB
Yaquin VK 2100 amp, McIntosh XR 5 speakers, Samsung BDP F 7500