I highly suspect it could be either a bad ignition switch or chip in the key. The symptoms do seem to fit perfectly: the security light is slowly taking longer and longer to stop blinking and let me start. I'm getting the car checked with a diagnostics tool today, perhaps if there is an error code as to why the light stays on while I drive that could help.
If it is in the ignition, what part exactly would need to be replaced? Is the decoder in the ignition switch?
As for the security system as a whole, I suspect that the shop probably assumed (maybe incorrectly) that the security system just went funky (without further diagnosis of the issue). I want to try and call them up and get some more info.