Sounds like you may have a bad PATS transceiver. They can be replaced and they're not keyed to the car so won't change your PATS program. They're about $60. They don't usually go bad but I have seen them get damaged.
My understanding is the flashing lock icon means the PATS system can't read your key. I'm assuming you've tried all your keys on the rare chance one is actually messed up.
> Catching up on the rest of the thread, I see it's fixed after flashing your tune. Odd. Unless your tune actually addresses the PATS system, it shouldn't have done anything. Possibly just resetting the system helped.