one day, after using some commands as: player.setav smithing 100, player.addperk, player.additem, tcl and tgm on my cheat character,some places like Whiterun the sky is simply water, some places like rorikstead which the sky looks like a reflected ground but still there are still some normal parts which weren't affected. BUT this continued in all my saves and its really anoyying.

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I wouldn't think those console commands would be the issue, but cheats and shortcuts can do weird things to a game so you never know. What mods are you running?