In your configuration.h, down near the bottom will be settings for LCD screens and buttons. For mine, the non-graphical lcd, I changed these two lines:

#define ENCODER_PULSES_PER_STEP 2 // Increase if you have a high resolution encoder
#define ENCODER_STEPS_PER_MENU_ITEM 1 // Set according to ENCODER_PULSES_PER_STEP or your liking

Play with those numbers to see if you can get it working better.