Not all encoders are the same. Depending on your encoder, you may need to alter your firmware for it to properly pick up all the rotations of your encoder.
By default, the encoder resolution is set to 4. If you use the EC11K Industrial Encoder that we sell on splitkb.com, you should use a resolution of 2. If you don't, it will seem to drop every other action when you rotate the encoder.
Add the following to your
// EC11K encoders have a different resolution than other EC11 encoders.Compile your firmware and flash it to both sides of your keyboard, and the encoder should work properly again.
// When using the default resolution of 4, if you notice your encoder skipping
// every other tick, lower the resolution to 2.
#define ENCODER_RESOLUTION 2