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I am not from Intel and I don't use Kodi nor Harmony Touch. However, I would question whether something else might have changed when you said BIOS 38 to 40. For example, is the Harmony still set to whatever setting produces codes to be like Windows Media Center RC6? Do you know the remote "ID" which is necessary for the registry entries in Windows such as 1 (typical default of Microsoft remote but MS can be set to other numbers) or 8 for Xbox remote, and is such number entered in the appropriate registry entry (or is the registry set to 0 - universal)? Did the CIR device driver stop loading - perhaps related to recent weird posting of an ITE Tech CIR driver in Intel's Download center (rather than the proper Nuvoton CIR driver)?
There was a BIOS change around 35-37 which added some CIR settings in the Visual BIOS pages, which I believe are only related to Power On; I believe that device drivers still control most aspects of CIR when an OS is running (and that the BIOS only got involved because someone wanted functionality from powered off state).