First of all...nice ryde!!
From reading other forums for a while now that spoke specifically about the RT SM5 the first guess is a software update "may" help. All depends on if the update has already been loaded of course. At your 600 mile dealer check, for the amount of money your spending make sure you ask them to check if your ryde has all the updates. I would also have a discussion with them about your concerns. Any reputable dealer (not all are) would listen to what you have to say and make it right. If it turns out you have the latest upgrades (not a given...see below) then during your conversation about the performance at low RPM's it may trigger the mechanic to look just a little closer...maybe there's an issue with the spark plug wires or even fouled plugs but that would be rare I'd think..
I bought my 2009 RS of the showroom floor about a month ago and 2 weeks later when I took it in for the first Spyder lobotomy...er check up I didn't even have to mention these things. The mechanics checked without my having to say anything and it was updated with the latest software per the specks. That showed me two things...they are very thorough and want my business.
With an RT-S are you using the higher octane? I've heard you can use both low and high octane but the RT's like the higher in general. Also...any Ethenol in the gas? Pure 100% gas (if you can find a station with it) seems to make the Spyders run better.
Bottom line..take your 600 mile dealer tune-up as a golden opportunity to ask
TONS of questions!