I'm having the exact same problems on a D5425WYKH with Windows 7 x64.
Moreover, i also have problems installing the new USB3 drivers from June 19th. it gives an error and tells you to abort the installation process.
Rebooting doesn't help at all.
I am not from Intel but I noticed that CIR driver and I think Intel must have posted it by mistake - it says ITE instead of Nuvoton (I suggest stick with the Nuvoton).
Regarding the graphics, you have listed different version number in the title (36.21.4222) vs the first line in your message (28.24.4229) - I do not see a 4229 driver in Download Center so maybe you should clarify for someone else who might know the answer.
I noticed the difference between ITE and Nuvoton too. anyway you HAVE to stick with the Nuvoton drivers because you don't have a choice ; the new drivers simply won't install.
The graphics driver says 36.21.4222 , but when you click the link, you'll see that it says 188.8.131.5229. also, the downloaded zip file is named 184.108.40.20629 too.
Yes, I can confirm the same problem with the new drivers.
It looks like Intel made a mess of it. In the description the graphics drivers are reported as being version 220.127.116.1122 but the download links point to driver files of version 18.104.22.16829, so a completely different version, probably not compatible with the D54250WYK.
And the ITE CIR drivers version 22.214.171.124 are also not compatible with the D54250WYK (at least not with mine).
Lastly also the USB 3.0 drivers version 126.96.36.199 seem to be not compatible with my D54250WYK.
I'm sorry, but i am talking about the drivers from this page : https://downloadcenter.intel.com/product/76977/Intel-NUC-Kit-D54250WYK
The "infrared driver version 188.8.131.52 for Intel® NUC with ITE Tech* Consumer Infrared (CIR)" won't install on windows 7 or 8, as other people stated above.
The link you posted is the old driver from 2013!
The Graphics driver page has been changed/updated. it used to show 184.108.40.20629.
The USB3 drivers are for people who use Windows 7 like me, and it won't install, no matter what (rebooting before installing, unplugging all devices from USB ports before installing, Changing the USB3 ports behavior from the BIOS,....).