It could be the portal theme is modifying the available space allowed for the iframe - my guess. Have you tried setting the iframe height to a set pixel value?
Also, take a look at portletbridge, it may be what you need and is configurable: http://labs.jboss.com/portal/index.html?ctrl:id=page.default.downloads&project=portletswap&category=.portlets.miscellaneous
IFrame height using pixel is working fine, but not with percentage.
Thanks. I will have a look to portletbridge.