Firstly, within the case, make sure you have connected S/PDIF OUT on the motherboard to the S/PDIF pins on the graphics card with the (provided) lead. The HDMI port needs to get its sound from somewhere.
Then, Control panel>Sound. Look throught the devices and right click the S/PDIF device and change to default. Save these settings and reboot. That should work. If it does not, goto the same S/PDIF device in control panel and with a right click/properties there is a tab for supported codecs. Untick all and leave only the Microsoft WMA Pro Audio option.
The app that did not want to play sound (in my case: Media Centre) needs to be restarted for the settings to work, which I achieve with a reboot.