Subtheme doesn't take settings from .info into account.

Hi.
Everybody knows this "The settings for this theme are currently served from a variable. You might want to export them to your .info file." message.
As stated here 2132039 we should type drush omega-export --revert, settings gets experted into .info file and the message goes away. That's true. When you go to your .info you'll see your settings as you made them on settings form. But when you go back to that form you'll see settings became default.

Steps to reproduce:
So let's say we want to turn logo off.
1. We go to settings page, turn 'Show logo' checkbox off, save settings.
2. Go to site pages, the logo went away. But that message about "The settings for this theme..."!
3. Go to console, type drush omega-export --revert, select your theme.
4. Go to theme .info and see settings[toggle_logo] = 0. Great.
5. Go back to theme settings form and see 'Show logo' checkbox on.
6. Go to site pages, see the logo went back.

I have layouts extension enabled, maybe this info may help.