This post is old, i know, but i'm having the same problem. The most i can say is i use EVB and CBBE for females.. i have seen posts about EVB having the neck seem issues. Hope that helps a little at least. i have not found a solution just yet
I know this thread is really old.. but I kinda feel the need to mention that just creating a shortcut for SKSE from the Skyrim folder and launching from there fixed the issue for me. Thanks a bunch!