It's because @array2 is an array of references - all to the same @letters array. @array1 is an array of references - but each element in @array1 is a separate reference to a separate array - that array is @new which is created each time through the loop.
As you modify @letters, @array2's members are changed because they are the same. But @new isn't modified again after it's assigned into the @array1 list, so you're getting a snapshot of each point through the list.
Unlike C, in perl when you create a new variable with "my", you actually get a new variable, unique from all similarly named variables that came before it, and unique from all dissimilarly named variables that came before it. You can take a reference to it, and that variable will not disappear until all references to it go away as well. After going through the loop, all you're left with is anonymous references to all the old @new's.
Hope that helps,
Update: Note to revdiablo - on original reading of the code, I actually expected @array2 to be the one changed, and not @array1. So maybe I understand the confusion a bit ;-)
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