Weird misalignment in my Susy layout

The elements I set the Susy span-column() mixin to, do not obey to it. They are misaligned ever so slightly. How do I achieve perfect alignment of my HTML elements?

Screenshot of full website misalignment

Detail : <header> and <nav> misalignment

Detail : <section class="main"> misalignment

Here is my Sass code

@import compass
@import susy
@import normalize


/* Susy Settings */


$total-columns  : 5             
$column-width   : 4em            
$gutter-width   : 1em            
$grid-padding   : $gutter-width  

$desktop : 12

/* Susy-grid-background override to draw out horizontal lines */

=susy-grid-background       
  +grid-background($total-columns, $column-width, $gutter-width, $base-line-height, $gutter-width, $force-fluid: true)


$base-font-size: 18px
$base-line-height: 30px
+establish-baseline

ul
  background-color: rgba(1, 0, 50, 0.1)

li
  background: rgba(200,50,0,.2)
  text-align: right

a
  background: rgba(0,220,0,.2)
  display: block

h1
  +adjust-font-size-to(90px)
  +adjust-leading-to(4, 90px)
  +leader(2, 90px)
  background: rgba(0,20,200,.3)


h1#logo
  +adjust-font-size-to(30px)
  +adjust-leading-to(2, 30px)
  +leader(0, 30px)

h2
  +adjust-font-size-to(25px)
  +adjust-leading-to(1, 25px)
  background: rgba(250,250,0,.2)


p
  +leader(1)
  +trailer(1)
  background: rgba(0,220,0,.2)


.page, header, .pagenav, .main, .pagefoot
  +transition(all .3s ease)

.page                                
  +container($total-columns, $desktop)
  +susy-grid-background



/* BREAKPOINTS */

+at-breakpoint($desktop)
  .page
    +susy-grid-background
  header
    float: left
    +span-columns(2)
    background: rgba(250,0,0,.2)


    h1#logo a
      +hide-text
      float: right
      +span-columns(2, 2)
      background: rgba(200,10,250,.1)

    .pagenav
      clear: both
      +span-columns(2, 2)
      background: rgba(0,140,250,.3)

  .main
    +span-columns(10 omega,12)
    background: rgba(0,240,200,.3)

  .pagefoot
    background: rgba(45,0,120,.3)
    +span-columns(12,12)

And my HTML

<!DOCTYPE html>
<html>                      
<head>
  <meta http-equiv="content-type" content="text/html; charset=utf-8">
  <link href="stylesheets/style.css" media="screen, projection" rel="stylesheet" type="text/css" />

  <title>Home</title>

</head>

<body>
  <div class="page">
    <header>
      <h1 id="logo">
        <a href="">
            "Designer Name"
        </a>
      </h1>
      <nav class="pagenav" role="navigation">
        <ul>
          <li>
            <a href="">
              <h2>
                work
              </h2>
            </a>
          </li>
          <li>
            <a href="">
              <h2>
                blog
              </h2>
            </a>
          </li>
          <li>
            <a href="">
              <h2>
                about
              </h2>
            </a>
          </li>
          <li>
            <a href="">
              <h2>
                contact
              </h2>
            </a>
          </li>
        </ul>
      </nav>
    </header>
    <section class="main">
      <h1 id="heading">
        Main Title
      </h1>
      <p>
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      </p>
      <h2>A New Title</h2>
      <p>
        Vertical grids are a compas feature. See the compass docs for baseline grid background. You won't be able to show both grids at once on the same element without a bit more work. Maybe we should integrate that somehow in Susy 2.0? Vertical grids are a compas feature. See the compass docs for baseline grid background. You won't be able to show both grids at once on the same element without a bit more work. Maybe we should integrate that somehow in Susy 2.0?
      </p>
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      </p>
    </section>
    <footer class="pagefoot">
      <p>Made by</p>
    </footer>
  </div>
</body>
</html>

Susy grids are (by default) fluid on the inside. All fluid grids suffer from some amount of sub-pixel rounding on the browser end. That said, what you are mainly seeing is sub-pixel rounding on the background grid, which is normally worse than the actual element-rounding. That is noted in the docs - the grid background is a rough guide, not a pixel-exact ruler.

Susy also has isolation options, which can be used to stop sub-pixel errors from compounding.