I think if you edit your preferences.txt file, located in 'Your RTW folder\preferences' , and you change the show_banners:true entry to false , then the red borders disappear as well as the little banners that float above the units on the battlefield.

Sometimes when you install a mod, they include a preferences file that over-writes whatever you were using before, so it may be the case that the banners were changed to false when you installed the sky-mod.