03 Cobra stalling during deceleration

I did a search on this topic, but couldn't find one that matched my problem.

I have a '03 Cobra that is stock except a JLT intake and a catback, which were on it when I bought the car. I've owned the car for 7 months and haven't had any problems with it until a couple days ago. The problem I'm having is the car will stall out when I am decelerating to a stop with the car in neutral. It doesn't matter if I have the clutch pedal pushed in or not. It only happens 1 out of 4 times or so, mainly when I am braking from higher speeds to a stop light, like when I get off the freeway. As I get down around 15-20 mph the RPM's start "searching", jumping between 500 and 1200 RPM for a couple seconds, and then it stalls out, but it always starts right back up again.

Any ideas of what the problem is?

Thanks for the input fellas, I will take the car in and have the ECM flashed and check into having a custom tune done for my car.

Good point, they want $80 to flash the PCM, and that doesn't include diagnosing it. A diagnostic is an additional $90. Dealerships are so lame.