***SOLVED***

My original code used the text method to draw the rectangle. It so happened that most browsers and some pdf viewers do not see this as a problem and render the line of text and the text over the rectangle (as desired). But apparently other pdf viewers are less forgiving of this.

use PDF::API2; 

  my $pdf = PDF::API2->new();
  my $page = $pdf->page();
  my $text = $page->text();
  my $font = $pdf->corefont('Helvetica-Roman');

  $text->font($font, 16);
  $text->translate(50, 620);
  $text->text('Print some text');

  # define rect with gfx
  my $rect = $page->gfx;
  $rect->rect(50, 560, 400, 18);
  $rect->fillcolor('#000000');
  $rect->fill();

  # Go back to text
  $text->fillcolor('#ffffff');
  $text->translate(62, 565);
  $text->text('Print text in rect');
  $pdf->saveas('test.pdf');
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