I've had this happen from time to time, though otherwise my Pro 3 behaves just fine. Seems like when it first starts up, sometimes the software assumes very high values for several parameters e.g. filter wide open, or osc pitch +700 (seems like zero would be a better power-on default for that), so that when I first turn a knob which is a potentiometer (not an encoder) it may jump to that high value.
I now prefer relative pot mode, which reduces odd jumps, but still this power-on default of values seems to contribute to sudden jumps.
What I do: right after power-on, I turn every pot back and forth a little, so that I see the values change in the display. If any knob is way off from where I'd typically want it to be, I'll move it to that position. I don't care what values are shown after all the knob-turning or if they're way off from the program's values, because right after turning every knob, I change to another program. Now the software seems to be aware of program values and also where all the knobs are positioned - no more big-value jumps.