I'm not sure if your problem is exactly this, but I think I've experienced something like your problem. I had once tried to drunkenly assign my minilab hardware encorders manually to the encoders on display in the analog lab software. When I woke up the next day, a couple knobs weren't working properly at all and I couldn't figure out why.
I clicked on midi assign mode after a few hours of frustration and discovered that I had left some of the encoders in the software assigned as relative knobs (which do not work for most functions in the analog lab). So as an example, lets say that analog lab was under the impression that encoder 11 was to be understood as a relative encoder.
Most encoders in analog lab need to be set to absolute value, which means turning all the way left will descend to a preset minimum, and turning right will increase to a preset maximum (usually 0-127). The result of this drunken confusion (after I reset my keyboard to the absolute value factory preset) was that when i turned knob 11, it would do nothing and then suddenly jump to full value, which pissed me off.
What was happening was that analog lab was expecting a relative value. relative value mode only goes from values 60-64, or something like that. This mode is intended for controls which have no limit, like scrolling through a list of patches, or something which has more than 127 options. when you turn the knob right, the encoder keeps sending values 62, 63, 64, reset, 62, 63, 64.. turning left will get you 64, 63, 62, reset, 64, 63, 62... (or something like that, I don't remember the exact values). this is to simulate unlimited increase or decrease in values for the purpose of scrolling through a large list (like presets..)
absolute value mode has a minimum of 0 and a maximum of 127. This is the mode for controlling effects and synth parameters. when I turned my knob to the right, nothing happened until I hit the expected relative value range in the low 60's, and then when I cleared through that range the setting on screen went from 0-100 instantly.
Anyways, what it sounds like is happening to you is that you have encorders in analog lab which are customized to accept relative values, and your physical keyboard encoders are set to absolute, or vice versa. You should reload a factory template in your keyboard in midi control center, and then manually re-assign all the on screen encoders to your physical encoders in analog lab. if you have the minilab like me, you'll want to have knob 9 set to relative 1 mode, as it functions as a scroll wheel in the analog lab.
