I've also been having this problem.
Mac OS 10.13.3
Sublime Text build 3157
It comes and goes. Sometimes it takes many tries for it to start with preferences available, other times it stays for a while. I've checked the console but there's no errors. Sometimes it comes back if I remove a plugin and then re-add it. It's very inconsistent and rather frustrating. What conditions cause Sublime Text to grey the preferences? Maybe there's a race condition in loading things back in that causes it to be unhappy or something? I don't know, just guessing.
For a while it was coming back when I removed Sublime Linter - Stylelint, but even now I've just removed it again and it's still greyed out.
I also tried removing all packages, and it was still happening.