I am very glad I came across this post, as I thought it was an isolated issue. I have a KERMA TDI tune in my 2011 JSW 6MT, and the tuner and I have been going through iterations on the so-called stumble I experience during light load, most noticeably in third gear, at around 1400, 1700, and 2000rpm. At first, the symptoms were shuttering in acceleration, then his subsequent tunes have quelled the shudder to more of a quivering, similar to the effects of braking on warped rotors. I decided to go back to my original tune in the meantime, and one time noticed a SLIGHT quivering at 6th gear, 1400rpm, light load, up a hill. Kerma has briefly suggested a throttle motor that's going out, but again, i only felt this symptom once.
my $0.02