I have noticed when I pop popcorn some just doesn't get done as fast. Why?
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Variations in water content, thermal conductivity of outer skin [if externally heated; microwave absorbance for nuked popcorn], strength of outer skin, and variations in how fast steam degrades the strength of the outer skin, will be the biggest ones.
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Popcorn kernels are like humans, they're made up of different races. The blacks are mentally slower and therefore pop slower.
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Just the nature, they're not all going to pop up at the same time because the heat will take time to spread to each kernel.