I had the same flicker problem with my D54250WYKH1. I'm using Windows 7 Ultimate 64bit, Windows Media Center with a SiliconDust HDHomeRun Prime 3 tuner. The local channels worked fine but the pay channels like History, HBO, etc. would often have a flicker or strobing effect.
One thing that helps a lot is to disable Contrast Enhancement. The Intel control panel for the HD 5000 (11-2014) is hiding this setting. Right click on your desktop and select graphics properties. This should bring up the Intel hd graphics control panel. Click the video icon, then click the down arrow in the upper left corner of this window. NOT the down arrow next to current settings, but the down arrow right next to the word Video. Select Image Enhancement, then select Advanced. About half way down the screen is the Contrast Enhancement that needs to be disabled. Don't forget to select apply and yes.
Other unrelated tips for using this NUC box as a HTPC: Use a wired network if at all possible. Try a short usb2 extension cable on devices that don't work properly on the NUC's usb3 ports. Google Shark007 and install the free codecs to play many more video files within Windows Media Center. HP media center remote, EventGhost, Logitech K400.