I recently got back from a trip with my '08 GT Auto. During the trip coming to a stop I noticed when I had been cruising at highway speed the transmission will pop and make a whining noise. I never noticed this when my car had a stock tune. This only happens when coming to a stop from a high speed. Driving to work of a morning I usually cruise around 55. Today I drove on a highway (atleast 70) a good distance as I sat in traffic it wouldnt do it but when I got up to speed around 55 then slowed down it would pop and whine going into second or maybe first. I am running a SCT strategy tune right now but also can recieve Bama tunes. Is this a normal thing? Normal thing with tuners? or should I call SCT and get a specific tune made for my car?

2008 GT Ford Racing 90mm Intake FR500s mufflers.