I have this problem. I'm working on this mod that changes the interior of Rethan Manor completely. The problem is when I work on it and close it the first time, it's fine when I view it in game. but when I reopen same mod in the Construction Set, it has the vanilla Rethan Manor features as well as the new ones. My laptop is a Asus Republic of Gaming and it has Windows 8 (I tried to find a new computer with Windows 7, but I couldn't)
Has anyone had this problem before, and what is causing it?