The last column doesn't increment "regardless of what $ne is", you can see that 214 is repeated twice, and so is 216. That's because $ne was different for the first of them and the program incremented a different value in the hash, but it wasn't incremented enough to change the max, so the max stayed the same.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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