This is were some people just don't get it. Setting speakers to "small" only means that you can play around with the crossover freq, usually 40,50,60,70,80,90,100,120,150,200hrz. Setting them to "large" means no high pass filter so the speaker runs unrestricted and will receiver freq under 20hrz. If you have a tower that can play down to 47hz for example you have to set it to small so you can cut it off at 50hrz or 60hrz.
Room correction isn't perfect all the time. Sometimes re running it can improve the results, you can always tweak your crossover setting after running the RC.
When I've run Audyssey XT32 it got my setup almost perfect. Only issue is it had my left surround 2 ft further back than it really was and had them set to 50hrz (which isn't a problem because they are capable large monitors).
chrisinmo re run it and double check it.