Could it be the head-slappingly obvious tromping all over $_ ?

    my  $checkbox = 1;
    $_ = 'Wowza';
    print "Before the loop we see \$_ as '$_'\n";

    if( $checkbox ) {
        while( <DATA> ) {
            chomp;
            print "  We see \$_ is '$_'\n";
        }
    }

    print "After the loop we see \$_ as '$_'\n";

__DATA__
There I was, minding my own business, when ...
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will output

Before the loop we see $_ as 'Wowza'
  We see $_ is 'There I was, minding my own business, when ...'
Use of uninitialized value in concatenation (.) or string at jonnyfolk1.pl line
18, <DATA> line 1.
After the loop we see $_ as ''