SagePay iFrame Theme Integration
So I had a couple of people asking about this here and on drupal.org - so I figured it would be easier to just tell you what I did.

in commerce_sagepay/inc/commerce_sagepay_server.inc around line 120 there is a piece of code that reads:

  '#markup' =&gt; '&lt;iframe style="width: 600px; height:500px" scrolling="no" frameborder="0" name="iframe_sagepay" id="iframe_sagepay" src="' . url('commerce_sagepay/sagepay_waiting_page') . '" /&gt;',


I changed this line to 

  '#markup' =&gt; '&lt;iframe style="width: 600px; height:500px" scrolling="no" frameborder="0" name="iframe_sagepay" id="iframe_sagepay" src="' . url('commerce_sagepay/sagepay_waiting_page') . '"&gt;&lt;/iframe&gt;',


in other words - explicit close the iframe tag.  It solved the problem for me.  

Hope this helps someone.