I've run into the same problem with my older Polks. I've come to the conclusion, correct or not, that the auto setup is able to get more bass extension from the surrounds suported by the subwoffer than it gets from the mains so it concludes that the surrounds are larger speakers and need to be switched with the mains.
I've found two work-arounds,
one (as Gonk suggests )setting the mains to small with a higher crossover ( 60hz seems to work fine with my RT2000s)
I've also tried turning the subs off and seting sub-woofer to "no" with the mains set to large.You then need to hand-tune the subs.
Of the 2, I've found I prefer the first option as the RT2000s can get a little boomy when set to large but behave pretty well set to small and crossed over at 60hz.