I have been unable to replicate any issues with adding a portal link to an email template. Here are the steps I followed;
Navigate to Customize -> Portals -> Edit an existing Portal. Here you will see 'Get sign-in page web address'. Click on this link and copy the URL that is provided. You can then paste this URL in to your email template.
By following these steps I successfully sent out an email with a link to the portal login screen.
I hope this helps. If you are still having issues after following the above steps please let me know.