ATMEGA32U4 Breakout Board Issue - Analog Pins as Digital

Thanks CrossRoads.
I double checked my pin assignment in the code and it is accurate to my wiring and the pins_arduino.h

Although while double checking my design to the pins_arduino.h i noticed some duplication of port usage for A6 - A11 (see below)

CrossRoads:
const uint8_t PROGMEM digital_pin_to_port_PGM[30] = {
PD, // D0 - PD2
PD, // D1 - PD3
PD, // D2 - PD1
PD, // D3 - PD0
PD, // D4 - PD4
PC, // D5 - PC6
PD, // D6 - PD7
PE, // D7 - PE6

PB, // D8 - PB4
PB, // D9 - PB5
PB, // D10 - PB6
PB, // D11 - PB7
PD, // D12 - PD6
PC, // D13 - PC7

PB, // D14 - MISO - PB3
PB, // D15 - SCK - PB1
PB, // D16 - MOSI - PB2
PB, // D17 - SS - PB0

PF, // D18 - A0 - PF7
PF, // D19 - A1 - PF6
PF, // D20 - A2 - PF5
PF, // D21 - A3 - PF4
PF, // D22 - A4 - PF1
PF, // D23 - A5 - PF0

PD, // D24 / D4 - A6 - PD4
PD, // D25 / D6 - A7 - PD7
PB, // D26 / D8 - A8 - PB4
PB, // D27 / D9 - A9 - PB5
PB, // D28 / D10 - A10 - PB6
PD, // D29 / D12 - A11 - PD6
};

Does the Leonardo do some kind of multiplexing on those pins?
I did notice in the datasheet that these are ADC8 - ADC13, but as i understand you either would use them as A6-A11 or D4, D6, D8, D9, D10, D12 not both.

Also asked this in the Adafruit forum and got this answer about the lack of Digital support on Analog 0-5
"this is a bug in the leonardo support for Arduino - its still beta so we suspect it will be fixed when its out of beta "
"this is part of the IDE itself, no idea how to fix it."