So here was the solution. In the BIOS when the PC boots up you press F2. Find the section that has USB Emulation and make sure it is disabled. Not sure what this is doing but I turned it off and it would boot to the standard install fine.
I came across another issue after the install completed though. I would get to the login screen, then login, and hear the standard ubuntu login, but all I could see was the mouse and nothing else appeared on the screen. I've had a simliar issue before with the free & open video driver not working, so what I had to do was press ctrl+alt+F1, this will bring you to a console shell where you can login from there. You will get a terminal once logged in. From there you have to do:
sudo apt-get update
sudo apt-get install xserver-xorg-video-ati
This should install the latest ATI drivers from the net. Once they are finished installing then just do a:
This should start the reboot of your machine, this time try and login again and hopefully it will work.
Note, from the comment below: I have found that after ubuntu is installed and everything is running fine, if I turn on USB emulation for some reason Ubuntu can't boot. Not sure why but I don't need it so it doesn't matter to me.