Problem with EEC not recognizing Key

I am having this problem where my EEC is not acknowledging my keys as being valid and as a result, the engine won't turn over...cranks like normal, but won't start. And while it's doing this the little "THEFT" light in the gauge pod flashes. In any event I took it in to the dealer on Monday morning and they told me it was my aftermarket alarm system interfering with the TAPS system. They disconnected the alarm's ignition kill and the car started several times yesterday afternoon and evening. Then this morning, when I was trying to get to work, it did the same thing all over again. So I had it towed to another dealership and they are looking at it now.

Has any one else experienced this problem? Do you know what the cause is and/or how to fix it?

Thanks.