In your code they were both undefined and I understood this by reading the code and understanding the error message. Which says clearly there is an undefined value used in a numeric comparison aka ==. There is only one thing that gets compared numerically in that line

$fix[$k]=1 if ($breakpoint{$chr}{$i}==1);
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Now if that condition is false then $fix[$k] will also be undefined because it is never set to something else elsewhere. But later on you use it in another numeric comparison

$S[$k]=0 if ($S[$k]<0 || $fix[$k]==1);
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And that triggers the second warning. My fix works so that I check for definedness of the value in the hash and making sure all values in the @fix are defined (either 0 or 1 instead of undefined and 1).