OK, some more info.
After a couple of hours messing around with this I seem to have gotten things working.
1. My Harmony One has been using the "Microsoft Media Center" remote profile for years (and has been working with an older i3 based HTPC with CIR) and has always been able to power toggle the NUC since I put it in close to a month ago.
2. Update to WY0027 broke this functionality.
3. Nothing I would try would get it to work. In desperation I installed MS Windows on another drive and that still did not work.
4. I added another activity with MS Media Center and still no dice.
5. I added another device in the Harmony setup with "Microsoft Media Center Extender". Using this device, all of a sudden magically the NUC started working in Windows. I put the other SSD in with OpenElec on it and that is now working too.
Hopefully this information might be of some use to others. I can only suspect that this new FW version re-programmed the onboard Nuvoton controller with a newer firmware version and as a result it stopped working with the much older IR code. Thankfully it does appear to work with the newer Media Center Extender codes.