Tell me more about what is configured here. Reading the terms you are using I am inferring you are using Pega 7 application embedded into your company portal using an IAC gadget or "Web Mashup"
What version of Pega 7 is this?
Are you using a DocType in your top level web portal?
Do you have compatibility view turned on?
Pega 7 is designed with Standards mode in mind using the HTML5 DocType. So if your top level portal is also designed with current standards you should not have this issue. If your top level portal or IT settings is trying to force a different/older mode, then that is likely your root cause, because your Pega 7 app will be forced to inherit said mode.
I am more concerned with running in the IE5 document mode, as that is Quirks, and will cause you problems in Pega 7, with or without Web Mashup involved.
But you are also correct that violating same-domain origin policy can cause a blank frame. However, I would expect you to have this issue with other IE versions as well, and not have it be specific to IE11.