Edge in IE mode - Different behaviour if set up manually vs GPO

[milnorr]

I am trying to get Edge in IE work on our web app. 

If I just set it up as Edge and manually go to the default browser settings and the app URL it seems to work ok. If I set it up on the GPO with 'configure internet explorer integration' and 'configure the enterprise site list' the app opens in IE mode but certain features do not work such as opening .msg files and session handling. 

 Are these GPO settings putting in zsones that the default settings are not? any ideas?

[#2]

@milnorr Hello!  I'm not sure about the exact issues you are having with IE mode but we do have some documentation for troubleshooting IE mode, Internet Explorer (IE) mode troubleshooting and FAQ | Microsoft Docs and also Associate file extensions with Internet Explorer mode | Microsoft Docs.  

Also, if you run into an issue with IE mode you can contact App Assure at https://aka.ms/AppAssure and they can help you with your problem.  Thanks! 

-Kelly