Mainstage 3: Samples sound different on various midi controllers

Perhaps the controllers that do not sound well do not have touch sensitivity - i.e. velocity capability and are therefore sounding the notes all at same velocity despite how you are playing the keyboard. Use the app "midi monitor" (free to download) to examine what the controller is outputting and pay attention to whether or not the velocity changes depending on how hard you strike (fast) the keys.

I suggest you examine the midi messages being sent by each controller and confirm that they are identical in all respects using midi monitor or other method.

Is this only happening when using Kontakt?

I've never really thought about this before but I wonder if the controllers causing the issue cannot transmit note traffic fast enough and/or are limited to a certain number of simultaneous notes (polyphony?). When viewing the midi traffic perhaps look at the timing and also if there are notes missing.

Good luck!