About the James Blunt song- I just created the sections in a fixed pattern, like, 2 sections in everey chorus if I remember correctly.
I highly suggest you guys just retune your guitar AFTER attaching the capo. RS just has some problems detecting notes after using capos for some reason. I just pause the song before the songs start playin' and just retune my guitar with the precision tuner of the pause menu while the capo is on, making sure each note is as close as it could get to 0. Make sure the pitch is not too sharp.
I actually got a 98% rhythm score in this song, so I don't think there's any bug or anything, it's just the RS note detector of the higher notes with the capo on.