While Manual upgrade of a MID Server below are properties which many cause issues.
1.) Folder/file permissions to the installation folder.
2.) Old MID Server Services are still active in memory
3.) MID.Pinned.Version parameter is manually set in the old 'config.xml'
If the 'mid.pinned.version' parameter is set to older version and if you try to manually upgrade the MID Server with that 'config.xml', it will try to downgrade and corrupt the installed files.
Make sure "mid.pinned.version" parameter is not set or not defined in the 'config.xml' file