You need to create the output channels inside kontakt and save it as the default configuration.
Click the + button, make them 2 channels (mono is buggy) and set the quantity to as many as you like. Personally I just maxed it out. Make sure to click save as default, this is the important part. When Pro Tools loads the plugin at startup, it will open up the number of outputs saved in the default configuration.
After doing this, any other configuration of outputs can exist inside each instance of kontakt as long as it fits within the number of outputs saved in the default configuration.
Code:
55 stereo outputs...
..