Flat spot in rev range since new alternator fitted

Hi
Last week I had to have a new alternator fitted to my '94 Mazda 323F V6 2.0.
For a few weeks the battery charge warning light had been faintly glowing
intermittently then stay off for a few weeks. Finally it would stay on above 2000rpm. Found it was overcharging after I had gone through two sets of blown headlamp bulbs in a week.
Since the new alternator was put in I've noticed a flat spot during acceleration.
As I get to around 4000rpm there's a moment of hesitancy - the acceleration flattens and then I feel a lurch as it picks up again.
Its very brief but nevertheless noticeable and irritating. The car has never done it before.
Is it possible the new alternator could cause this?
Or is it a sign of damage to other components caused by the overcharging of the previous one? Although I didn't have this flat spot while running with the old alternator.
Your thoughts would be appreciated.
Thanks
Ian
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