There are two possible problems here. I had a similar problem with my 2004 Bentley Arnage. My problem was that the terminal contacts in the remote had corrosion build on up on them. Enough power from new batteries to light the light on the remote, but not enough power to effect the unit in the dash. Mine also works only the Navigation system and not the audio head unit for some reason. Changes are, there is a frequency setting required somewhere between the two various units and the remote and one or more is likely out of sync in your case, likely due to the replacement.
G-Man
February 2010