my @header_present=" "; #clearing the data here

This places one element into @header_present, which is a string consisting of a single space. Arrays are true if they contain at least one item, that's the case after this piece of code.

The right thing would be not to assign anything; my @var automatically creates a new, fresh, empty array.

If you want to clear an array later on, you can write

# recommended:
@var = ();

# or a bit more excotic:
$#var = -1;
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You can read more about that in perldata.

You would do well to adapt a consistent code indenting style. See perlstyle for example.