Thanks for the information so far. I had the capacitor rotated from C17 to C18 so now it is using the Inverted-F antenna on the TWR-KW21D256.
To test simple TX and RX continuous transmissions, I've modified the Wireless Uart example, so the TWR-KW21D256 is successfully receiving from another Zigbee dongle and it is also successfully transmitting which the Zigbee Dongle receives. I also have a USB-KW24D512 as a packet sniffer to capture packets in the air. So now using the Inverted-F antenna on the TWR, it is still successful in TX and RX.
But the same code on our prototype board, it neither receives nor transmits, the packet sniffer doesn't show anything transmitting from the prototype board and when I transmit from the Zigbee dongle, it doesn't receive anything either but the packet sniffer shows the Zigbee dongle's transmission. Also this is all in very close range, everything is within 1-2ft of each other.
So with the software successfully working on the TWR board and for the most part on the prototype board (GPIO and UART), it seems like this is a hardware issue?