frequently, there is an led light on the receiver of the door opener.
Put the remote very near the receiver, and press the remote button and see
if the receiver led lights. If it does, then you have confirmed that your
replacement battery is ok, and that the remote sends out a signal of some
sort. Then you would have the hint that it is indeed a programming glitch.

If the receiver led does not light with the remote activated, I would first
check the battery contacts, to make sure they are shiny clean, and double
check the polarity. If this doesn't work, then I think I would run to ebay
real fast and see if you can find a replacment remote. Of course, you can
always contact the manufactuer for a replacement.

Can't think of much else right now.....

Let us know if you get it solved...

James