Hi @carlesls.,
You can check if the KBI is being configure correctly in the Peripherals+ tab.
Also, the KBI only manage one interrupt flag, if two interrupt happens at the same time in the same KBI this can cause only one of them to trigger, this same flag should be cleared every interruption, if this is not done the code will constantly enter the IRQHandler.
I made some test on a FRDM-KE02Z with the configuration you share, and all work as expected.
Is there any other configuration on your project that could affect the KBI peripheral?