The EQ can be applied to the Music our the Input (Microphone or Instrument through adaptor). Please Ensure you have the Music selected. There is a selector to choose to the right of the On/Off button. You will see the source in text at the bottom right of the EQ screen.
You can also Tap the Song Title and reveal the Song Info view. The Settings will show the value of the EQ for Music and Input.
Send us a screen shot through Help > Email Support and we will figure it out.