I recently purchased two aftermarket remotes for my 99 Accord EX with the factory installed security system. Programming is pretty easy, but it seems the trunk open function only works on one of the two remotes. All other functions work well with both remotes. I even tried programming the new remote as if it were a stand alone and the trunk function still doesn't work or should I say it might work once in 20 or so attempts. I hold the button down for several seconds also. I contacted the company and had a replacement sent to me just in case I had a malfunctioning remote. Same deal, the trunk open function does not work on the replacement. The company states this is a popular remote and they haven't had this issue before. I have only programmed two remotes and the limit is three. Can anyone venture a guess as to why a second remote doesn't work?

 

May still be the remote transmitter. For OEM, the transmitter for the 1998–99 Accord and the 2000–02 Accord look identical, but they are not interchangeable. The 1998–99 transmitter works the doors of a 2000–02 Accord, but it does not open the trunk.

It may be a similar issue with the aftermarket transmitter you have.

 

It has to be the second remote that isn't compatible. There are no numbers inside the case like the ones in the diagram you provided. Two of the chips have different numbers in the new remote as compared to the working one. I don't see how the company can tell the difference since you clearly describe the difference between the two remotes above. Maybe most folks don't use the trunk release and don't bother.