I am pretty sure you need to downgrade your IFrame module version - I think to version 3.x.x

Shane,

Have you thought about placing the iframe code inside a HTML module.  If placing it in the content area takes out the code then place it in >Module Settings >Header.

Attribute Specifications to Adjust Appearance and Behavior
  >src="(URL of initial iframe content)"
  >name="(name of frame, required for targeting)"
  >longdesc="(link to long description)"
  >width=(frame width, % or pixels)
  >height=(frame height, % or pixels)
  >align=[ top | middle | bottom | left | right | center ] (frame alignment, pick two, use comma)
  >frameborder=[ 1 | 0 ] (frame border, default is 1)
  >marginwidth=(margin width, in pixels)
  >marginheight=(margin height, in pixels)
  >scrolling=[ yes | no | auto ] (ability to scroll)

Here's an example:
<iframe name="inlineframe" src="float.html" frameborder="0" scrolling="auto" width="500" height="180" marginwidth="5" marginheight="5" ></iframe>

Regards
Mike Bussiere