It sounds like your internal site requires IE9 document mode which is still supported in IE11 on Windows 10.
Two options to set the default compat mode for that site to IE9:
If you can update the site code, you can add the following meta tag to all of the site pages to make it request IE9 mode.
<meta http-equiv="x-ua-compatible" content="IE=9">
If your intranet has managed PCs, you can use the Enterprise Mode Site List feature to add specific sites on your intranet to load in specific document modes in IE.