I also found that the only key is 6 (just the number 6).

The problem is that you are using the size of the arrays (eg. @quintic in a scalar context) as your hash keys. If you quoted the hashes thus:

$haystack{ "@quintic" }{ "@derivative" } =  \@zeros;
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Or used join something like this:

$haystack{ join ',', @quintic }{ join ',', @derivative } =  \@zeros;
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That might be nearer to what you are after, though it may not sure all the ills.

Note also that I've backslashed \@zeros to store a reference to the array, otherwise you are again storing the size of the array, not its contents.