New Computer Cannot Install Windows 8.1 from usb

Apr 26, 2014
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UPDATE: Windows 8 has now been successfully installed using the process
here.

My friend decided to make a new desktop to replace his old Macbook for general usage. As we're students we are given access to Microsoft's suite of products, including OS's and downloaded a copy of Windows 8.1 to save some money.

Using the Windows 7 Usb tool from Microsoft to load the iso onto a bootable usb we encountered an error when trying to install. Upon booting from the usb the blue Windows logo would appear and just sit there with no installation prompts, no loading circle, nothing at all for about 10-15 minutes until it's replaced by a clear blue screen. Leaving it to sit overnight lead to no progress and suspecting a bad ISO/usb we've tried redownloading the iso and changing the usb used to no avail. I've tried booting from usb using my own laptop and can successfully get past the blue Windows logo into the installation menu. As a check to make sure the hardware was running we decided to try installing Ubuntu and succeeded in installing the 64-bit 14.04 version of Ubuntu onto the new computer. While Ubuntu is running well he'd much rather have a version of Windows.

Specs:
AMD FX-6300 3.5GHz 6-Core Processor
MSI 970A-G43 ATX AM3+ Motherboard
Kingston 8GB (1x8GB) DDR3-1600 Memory
Western Digital Caviar Blue 500GB 3.5" 7200RPM Internal Hard Drive
Gigabyte GeForce GTX 650 1GB Video Card

Any ideas on what to try next as I am stumped as to what the problem could be.