Honda Factory keyless entry with alarm

I need help with my 1996 Honda Civic EX.  My Civic has the factory keyless entry and the factory alarm accessory.  As many people know the 1996-1998 civics had the keyless entry and alarm system going through the factory radio (I have an aftermarket stereo with factory radio hidden inside of the car).

I have had the aftermarket radio installed for about 3 years with no problems.  Recently, I tried to use the factory keyless entry remote to disarm the system and it will not work all of the sudden.  So, basically the system is stuck armed, and when you go to open the door with the key the alarm goes off.

*Note when I was walking up to the car I did notice that the dome light was doing some sort of a strange flickering like it was haunted.

The first thing I did was the check the battery in the remote and replaced it with a new one.  That did not work.

I checked the fuse box and found no blown fuses.

I checked the wiring going to the aftermarket and old radios to make sure no wires came undone, they turned out to be ok.

Basically, I am stuck with no signal going to arm or disarm the system. 

My question does anybody have an idea what could be wrong?  Could there be a malfunction with the factory radio? a bad relay? (if so, how do you check a bad relay?)

focalcivic!

I'm having the same issue right now and not really knowing what to do.  I was thinking about just pulling the fuse for the horn (for the neighbors sake), but does that make our Honda imoperable? Since you went through this very recently...I'd really ask if I can get your personal e-mail address so that I can talk to you for a few minutes.  I've called several dealerships what got confused because of the year of the car.  I even had one guy tell me that alarm was really the panic going off and that Honda of that year didn't have an additional alarm option to add to the car.  Needless to say, we'd didn't speak much more after that.

Please make contact with me please...my e-mail address is jimjam@nildram.co.uk  

My Honda is the exact one as yours, US specs and all.  I'm living in London with the US military and brought my car overseas.  If anything else, I'd love to know the number to the dealership or guy you spoke to.  Thanks!  Jim