Do you have the Launch Control box ticked in the Config Options menu? If so, it will limit 1st gear RPM pretty much every time you take off from a stop. Once you close throttle it thinks you are no longer launching and acts properly. It looks for Zero speed, a pulled in clutch, and fresh engagement of 1st gear to trigger the function. If you merely downshift to 1st, but are still rolling, the launch control isn't engaged so it behaves normally. Turn off the Launch Control, or set the RPM to about 9000 or so to alleviate that problem. Or...if you use the launch control for a Race Start, just soft pedal the bike or short shift to 2nd coming out of the Pits. Check in the Config Options for the Launch Control rpm settings. They should coincide to when the engine is refusing to accelerate further in 1st gear. Also, I went into the Tune settings and turned off my Kick Stand kill. I always pull in the clutch to start the engine, but sometimes the gear indicator sensor says it's in 2nd (probably should change the sensor... @%&%$$$$$$) and I warm up the bike on the kick stand. Eventually, after it's warm the sensor starts working properly and the problem goes away...right up until it's cold again. The plunger tip is probably worn. Otherwise it works properly.
Also, I changed out my shifter mechanism because it had some slop in it. I used a complete side plate assembly off a 959 with about 2000 miles on it. Direct swap across since the 959 is not much more than a reduced bore 1299 so a ton of parts swap across the 1199 and later series of designs. (even the new V2 still uses the 1199 Sachs rear shock, with different adjustment dials) The sloppiness went away and the shifting became much crisper. If you can use your fingers to move the shift shaft radially at all, the bushing is worn to the point it may start affecting your shift quality. I went to a ball-bearing foot lever just because the bushing was worn in the stock lever and it tended to flop. The bushing in the shifter shaft on the engine has the same problem, though it does have a second pivot point on the casing itself at the other end of the shaft, so things don't get totally wonky. Had the same thing with the bushing for the Brake lever as well, so swapping to an aftermarket rearset was a no-brainer.
Let me know if you get any 'surge' during the downshifts please. At higher rpm, above about 7000 for the DS, there might be a momentary surge in one of the 3-6 gears that I never truly got rid of. If it occurs, mark the rpm and gear selection, then go in and reduce your LEN options a little to get rid of it. Dropping them by about 8-10% should do the trick. It usually occurs when I am not hard on the brakes but just downshifting on a light decel. 4-3 I am thinking if my memory is working properly today. It could be that I'm not totally off the gas or that there is a braking parameter that makes things work better on hard braking vs soft.
