It seems that the navmesh slope is clamped to 60 degrees in Unity5.

In Unity4 it was possible to set a slope of 90 degrees but now it is clamped to 60.

This behaviour is now allowed again. However, it's disabled in UI by default. To enable it use this method from an Editor script:

[MenuItem ("NavMesh/Build With Slope 90")]
public static void BuildSlope90 () {
SerializedObject obj = new SerializedObject (NavMeshBuilder.navMeshSettingsObject);
SerializedProperty prop = obj.FindProperty ("m_BuildSettings.agentSlope");
prop.floatValue = 90.0f;
obj.ApplyModifiedProperties ();
NavMeshBuilder.BuildNavMesh ();
}

Fixed from 5.0.1p2 onwards.