Well I think I know what you mean but let me explain what is happening.... Intelliremote doesn't "eat" HID signals from the remote it simply listens and acts. Any other program listening can also act on that signal. What we do is disable the default MS behavior because what would happen is you would have Intelliremote do an action and then MCE do the action on the same remote command. This is known as "double button push".
Now if you wanted that back you could re-enable the MS remote and then mark Intelliremote commands as "Key Event = <none>" telling Intelliremote not to do anything with that key for this profile. You can read this last post in this thread on doing that.viewtopic.php?f=1&t=6130