Hah that was a bit of a schoolboy error, but thanks for your advice). I changed the default build of Arduino and it got over this problem. However, I now have another probelm, see below. If its obvious what this problem is then by all means let me know, but for know I will try and decipher this for a while and maybe create seperate thread if I can't figure it out:
Uploading via Bootloader
C:\Program Files (x86)\Arduino\hardware\tools\avr\bin\avrdude "-CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf" -v -patmega32u4 -cavr109 -PCOM3 -b57600 -D k.hex:i"
avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
Copyright (c) 2000-2005 Brian Dean,
http://www.bdmicro.com/ Copyright (c) 2007-2009 Joerg Wunsch
System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"
Using Port : COM3
Using Programmer : avr109
Overriding Baud Rate : 57600
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :
Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
Programmer Type : butterfly
Description : Atmel AppNote AVR109 Boot Loader
Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding