Common issue, the lack of proper implementation of this kind of technology by the receiver companies.
Apply cross-over. Try 80hz, and other settings if you wish. The problem was that Onkyo incorrectly assigns as large when the rolloff be found to be lower than 80hz, or at least that's how it is with MultEQ and MultEQ XT. So I presume it's an identical issue.
Even Audyssey would demand that you apply xover. As far as they are concerned, having a sub in the mix automatically means that your sats should be small.
Small vs. Large
While I'm at it, if the distances seem off, particularly the sub, just leave them be. See, the distance measurement by Audyssey is the sum of both physical AND electrical distance (filters, DSP, etc).