Thanks to Andy Pemberton for helping me with this one. It definitely had me confused for a couple days. This issue is specific to IE and only presents itself when you are exposing your portal over HTTP, but are accessing through an HTTPS load balancer or web server. The result is a mixed content popup from IE everytime you access a page. This is caused by an iframe shim being inserted by WebLogic portal for the automatic menu navigation. The fix is easy and straightforward, but finding the solution was not as easy.

To fix this issue, navigate in your Portal Web project to the Merged Project Content "virtual" directory in Eclipse which should be directly under the Portal Web project when viewing in the Portal perspective. Under that directory, navigate to framework -> skins -> bighorn -> msie. Right-click on the iemenu.js file and select 'Copy To Project'. At this point, the file will reside in your WebContent folder in the same path as above (framework -> skins -> bighorn -> msie). Double-click the file and find the line of code

shim.setAttribute("src", "about:blank");

and replace with

shim.setAttribute("src", "javascript:false");

The issue will now be resolved. There is a little bit of overhead for this call to be made for each Menu shim, but still much better than the previous error being popped up on each page refresh.