I've seen this mentioned here before. The consensus is that the auto set-up features of most receivers, while good and handy, are not perfect. If you're sure that you have all of the wires hooked up correctly, then don't worry about the polarity warning.
I'm assuming that this has a set-up microphone. The acoustics in the room may be throwing off the readings and causing it to think that the surrounds have reversed polarity.