By default Windows will handle most of the MCE Remote buttons, the arrow buttons, number buttons, etc ... But I've now figured out a way to stop this behaviour ...
To handle the MCE device Windows loads a series of device drivers onto the system. The main driver is the USB device driver, it provides access to the MCE device. Without it you can't use the device at all.
There are also a series of Human Interface Device (HID) drivers that are there to translate raw information from the USB device into remote button presses, keyboard and mouse inputs.
You can't disable the HID drivers but you can alter their settings to prevent them from acting on the button presses coming from the remote.
This process should work on all version of Windows that support the Microsoft eHome Infrared Transceiver. I've tested on Windows XP Pro and Windows Vista Home Premium and it worked on both.
However, please note that HIP, Girder and EventGhost can't use the default Windows eHome driver in Vista. On Windows XP these programs are fine, but these programs need the Replacement driver for Vista and I haven't been able to get the Replacement driver to work on 64-bit Vista yet, only 32-bit Vista.
Load "regedit.exe" and navigate to:
Then delete the keys from "CodeSetNum0" to "CodeSetNum3".
To make sure you can recover these keys easily should you want to you should save them by using the export function in the file menu.
Once the registry has been changed you will need to reboot for the change to take effect.
This same process can be applied to disable automatic keyboard handling. Just look at the other registry sections under the "Remotes" sections.
Now if you ever want to re-enable the automatic handling of the MCE Remote and MCE Keyboard you just need to put those registry keys back.