It sounds like a need for TRE. Do you have one installed? If not then read on.
If your bike is a little out of tune (fuel map to rich/lean) and there is no TRE, then you might aggrivate the timing retard that a stock ECU has on gears 1-3. The ECU retards these gears up to 5000 RPM to help increase traction and reduce smog. The TRE removes this retarding on low RPM timing and can really clean up the low RPM range stumbles like Hawaiibusa said.
Last year I was riding with friends in the hills. Going into a tight left-hander I shifted down to 1st with RPM's around 5-6000 with the throttle closed. In the middle of the turn I hit a harsh bump and my wrist cracked the throttle just a little at about 4500 RPM. The ECU came out of retard and gave me way more torque than I expected. The front end came off the ground while leaned over hard. The bike went straight for a tree so I closed the throttle hard. That stood the bike straight up and almost highsided. I was puckering up on the edge of the road at about 50 and brought it back in. That experience showed me the need for TRE. Now all my throttle turns give me the same power each time. Yes it is more, but it is predictable and you can get used to the additional power quickly.