Your regex is awfully slow. That's what it comes down to. You're inching forward character-by-character until you come to '##' or the end of the string. The regex could be made amazingly faster by just making this one change:

$str =~ /(##(?:.*\n)*)(?=##|\Z)/g
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That reads "lines" at a time until it gets to '##' or \Z. Another way you could write it (to be very fast) is:

$str =~ /(##(?:[^#]+|#[^#])*/g
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That doesn't even need the look-ahead.