The Arduino Zero's current build, 1.6.6, activates the Tx and Rx LEDs to indicate activity on the native USB port.
In previous builds these Tx and Rx LEDs remained unused by the Arduino core code, but could be activated in your sketch. If like me you decided to take advantage of these former unused the Tx and Rx LEDs for your own purposes, then it's necessary to deactivate the Tx and Rx pins on the USB native port.
Fortunately Arduino have wrapped the Tx and Rx LED's code in #ifdef directives in the native USB file. This means that if you comment out the PIN_LED_TXL and PIN_LED_RXL definitions in the Zero's "variant.h" file, it'll deactivate the Tx and Rx LEDs on the native USB port and your free to use them in your sketch oncemore.
Code snippet from "variant.h":
// LEDs
#define PIN_LED_13 (13u)
//#define PIN_LED_RXL (25u)
//#define PIN_LED_TXL (26u)
#define PIN_LED PIN_LED_13
#define PIN_LED2 PIN_LED_RXL
#define PIN_LED3 PIN_LED_TXL
#define LED_BUILTIN PIN_LED_13