Did anybody do any work on the door lately? Even if not with the aftermarket alarm install if they did a sloppy job on the wiring something might have come loose. I'd probably double check the wiring that runs under the sill plate to make sure everything that runs from the door to the alarm or whatever are in good shape and that nothing's come loose-even if everything in the door itself is hooked up OK the wiring under there might be borked.
Had some painful personal experience with something similar-a sloppy shop worked on my car and did a crazy sloppy job rewiring the door then when I tried to get them to fix it they claimed that they had already checked and that nothing was wrong when in fact they hadn't even tried to fix it.
Luckily the d-bag owner's wife was pretty nice and actually someone to take the car apart to check the wiring, and that's when I saw the joke of a wiring job they had done (think wires held together by just twisting the bare wires). If anybody's done work on the door or alarm before they might have rewired it poorly so I'd probably trace the wiring all the way out from the door to make sure everything's intact.
It sounds like it's something painfully simple but the hard part is basically tracing out all the wiring from the door. Also the T-taps sound a little suspect, might honestly be worth it to do some proper soldering or something. Something or another might not be working right with the install.
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