It could be two things.. If you copy pasted the switch and door that means it might have the same tag number? If it has the same tag number it might highlight both sectors and all sectors involved with that tag. Change the tag number.Or when you copy paste a sector sometimes the editor recognizes that and for easier purposes it makes it the same sector. In 2D mode press "M" for "Make Sectors" and click on each sector you want to separate. Make sectors takes sectors that are combined and separates them to be there own. This one probably won't work if the tag is the same on them though.
HalleFUCKINGlujah!
Duke I know you are finished with another Doom 64 map when you going to post it xD Hope you post it soon going to be really cool playing with Turok textures. Where are you at on the Hell's Keep project though?