If it's the same scene, you can stack, and then add the colouring...and effects. So, will look more uniform.
Also depends on colouring..
Many times, I feel stacking may add pixels.
Also, the 1st set you put looks more with pixels cos of colouring, the 2nd set is smooth, maybe you used pastel psd or less colours..
Try keeping minimum frames when you stack too.
Hope this helps
-madz
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