Alarm doesn't recognize either of my key sets, and neither remote works!

All of a sudden, both key sets touch off the alarm (car still starts) and the remotes do not lock/unlock doors, nor open the trunk.
WTF?
Batteries are fine.
I have instructions to re-program the remotes, but will that fix the alarm issue?
What ties these two seemingly unconnected symptoms together?
Appreciate any insight.

BTW, the help section has a script error and is not working. Can anyone remind me how to edit the addendum to my profile that appears under my posts (the description of my vehicles)?

Okay, I am assuming that I armed the security system when I last locked the doors (while the remotes where working).
Since the remotes were not working, I opened the door with the key. So, I am again guessing that the alarm went off because it was not disarmed?
Anyone have any ideas?

I plan on reprogramming the remotes, but don't know if the alarm will remain a problem.

There is a receiver in the trunk for the remote keyless entry. I believe mine failed on my 95 and it was plug and play from a junkyard 95 riv. And yes, if you lock the car with the key fob, and unlock it with the manual key, it will set off the alarm. Not sure if there is a workaround for that part.

Thanks, Dave, for your input.
I went to my shop manual to check out the module and came across instructions (page 8-680) to synchronize the transmitters. Apparently they can go belly up for a couple of reasons, one being repeatedly pressing buttons while out of range.
Anyway, all I had to do with each transmitter is press and hold lock and unlock buttons while in range for 8 seconds. Horn beeps and everything goes back to normal!
That's a relief. Thanks again.
Sean