We do not have anything in our App_Browsers folder that breaks any web browsers. I added this fragment:
<browsers>
<browser refID="GenericDownlevel">
<capabilities>
<capability name="cookies" value="true" />
</capabilities>
</browser>
</browsers>
which basically says if you see a browser you don't recognize assume it supports cookies. This does not affect known browser versions of IE and does not interfere with browser definitions updated by windows update.
I DO NOT recommend removing or modifying the /App_Browsers folder of mojoPortal, changes there require that the source code must be re-compiled as far as I know.
I am not aware of any problems using mojoPortal and IE 11 as long as the web server has all the windows updates installed. This thread is resolved and closed as far as I'm concerned.
If you think there is any IE 11 bug in mojoPortal, then try to produce the problem on our demo site, if you can produce a problem there, then start a new thread and explain steps to produce the problem, expected result and actual result.