This blog entry is about how I solved the problem where my Intel NUC D54250WYK wouldn't boot after I upgraded my BIOS from 22 to 25. (I should have paid to attention to the note that said, "Don't install this if you don't need it." However, I was installing Windows 8.1 and I wanted to make sure I had the latest fixes.)
The symptom was that the NUC would turn on, would flash three times, wait a few seconds, flash three times, and then turn off.
I was running the NUC with 16GB of DDR3 1866 (PC3 14900) Laptop Memory. This memory is faster than most users run, but recent versions of the BIOS are documented as supporting this speed of RAM.
I tried taking out one of the DIMMs, which had worked for me in the past. However, this didn't work this time. (If you try this, make sure you take out the correct DIMM. The NUC will operate on one DIMM, but this configuration is only supported for one of the two slots.)
Eventually I just left the NUC alone for half an hour in its reboot cycle. It eventually booted successfully and the problem did not come back.
Followup, Oct 2014: My system would crash every couple of weeks after I wrote this article. I finally ran Windows memory tests, which failed. I changed the NUC BIOS to slow down the memory and it worked fine after that.