I've never noticed them before today, and now in the Changes tab of all my projects, I have a "Roots Switches" item.
What is this? A couple days ago there was an 'incident' with my $userdir/.cvspass file. Basically, it got wiped through no fault of intellij. When I first went to do something cvs-ish, it prompted for the password and upon entering things were back to normal. Except now I'm seeing these "Roots Switches". the cvspass file might be a red herring, but it's all I can think of that has changed, and it's very close in time.
Perhaps I'm just blind and I've never noticed it before in several years of using IntelliJ.