if the remote fob has been dropped or "man"-handled...the chip inside may have come dislodged. This happened to someone one not to long ago. If you open the remote fob, you can check it and if its loose...re-seat the chip.
The keyless entry system has a seperate booklet and isn't really explained in much detail in the owners manual. I have the BMW/Alpine keyless entry instructions on my cardomain site...check it out...then check the chip in your remote: http://www.cardomain.com/ride/739005/3
(here's an example of one of three pages you should read & check out about the transmitter microchip replacement at link posted above...(#2) is the chip holder and probably has come loose)