Hard to say what is going on with your car without looking at the dyno sheet or test driving it ...
It could be almost anything.
But any time you change or alter something in the power train you are going to affect everything else as well.
Your car might benefit by the back pressure caused by the cats.
I had PPE long tube headers with no cats on my car ...
That combo created an easier exhaust flow with a smoother scavange, but at the cost of increased loudness, emission odors, and perhaps a little drop in torque.
With the tune - my car did have a pretty flat torque curve which all but eliminated the flat spots during acceleration.
Hope this helps...
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