Here is the verbose output, it does make me a little bit suspicious that it says its using the cstk500v2, is that the avrisp?
This is trying to load the bootloader, below this is where i load a blink program and that works
Arduino: 1.6.5 (Windows 8.1), Board: "Arduino Uno"
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v2 -Pusb -e -Ulock:w:0x3F:m -Uefuse:w:0x05:m -Uhfuse:w:0xDE:m -Ulfuse:w:0xFF:m
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 : usb
Using Programmer : stk500v2
avrdude: usbdev_open(): Found AVRISP mkII, serno: 0000B0026998
AVR Part : ATmega328P
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
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 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 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 : STK500V2
Description : Atmel STK500 Version 2.x firmware
Programmer Model: AVRISP mkII
Hardware Version: 1
Firmware Version Master : 1.23
Vtarget : 3.2 V
SCK period : 4.00 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0x1e950f
avrdude: erasing chip
avrdude: reading input file "0x3F"
avrdude: writing lock (1 bytes):
Writing | ################################################## | 100% 0.00s
avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x3F:
avrdude: load data lock data from input file 0x3F:
avrdude: input file 0x3F contains 1 bytes
avrdude: reading on-chip lock data:
Reading | ################################################## | 100% -0.00s
avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude: reading input file "0x05"
avrdude: writing efuse (1 bytes):
Writing | ################################################## | 100% 0.00s
avrdude: 1 bytes of efuse written
avrdude: verifying efuse memory against 0x05:
avrdude: load data efuse data from input file 0x05:
avrdude: input file 0x05 contains 1 bytes
avrdude: reading on-chip efuse data:
Reading | ################################################## | 100% -0.00s
avrdude: verifying ...
avrdude: 1 bytes of efuse verified
avrdude: reading input file "0xDE"
avrdude: writing hfuse (1 bytes):
Writing | ################################################## | 100% -0.00s
avrdude: 1 bytes of hfuse written
avrdude: verifying hfuse memory against 0xDE:
avrdude: load data hfuse data from input file 0xDE:
avrdude: input file 0xDE contains 1 bytes
avrdude: reading on-chip hfuse data:
Reading | ################################################## | 100% 0.00s
avrdude: verifying ...
avrdude: 1 bytes of hfuse verified
avrdude: reading input file "0xFF"
avrdude: writing lfuse (1 bytes):
Writing | ################################################## | 100% 0.00s
avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xFF:
avrdude: load data lfuse data from input file 0xFF:
avrdude: input file 0xFF contains 1 bytes
avrdude: reading on-chip lfuse data:
Reading | ################################################## | 100% 0.00s
avrdude: verifying ...
avrdude: 1 bytes of lfuse verified
avrdude done. Thank you.
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -cstk500v2 -Pusb -Uflash:w:C:\Program Files (x86)\Arduino\hardware\arduino\avr/bootloaders/optiboot/optiboot_atmega328.hex:i -Ulock:w:0x0F:m
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 : usb
Using Programmer : stk500v2
avrdude: usbdev_open(): did not find any USB device "usb"
Error while burning bootloader.