oh i wouldnt doubt it, sad the 'reflash' fixed it for a short duration. seems it could be a 'd clutch pack' issue, so i wondered if OP ended up having to go the route of repair or? its going to the dealer on the 14th so we shall see.
Not to beat a dead horse but... have to wonder what became of this for you? or anyone else thats had this issue. Bought a 26' JT a little over a week ago and am experiencing these same symptoms. low speed, 3rd gear, bit of a 'clunk' then revs, 'fine' if youre gassing it through gears. unsure how...