Just posted this over there for you. Not sure if it will help...
Did you update the drivers/MixControl software? That is imperative. However there are some complaints about the very latest version. I have the one preceding that and it works fine. Here is what the MixControl software is telling me on the splashscreen:
Scarlett MixControl = Version 1.1.128.0
Driver = Version 2.3.0 API 3.0
Firmware = Version 198
That said have you maybe on one of the other Mix tabs on the top left of the screen thus hiding the active mix? Have you checked your routing settings and compared them to the examples in the manual? The routing settings controls are below the mixer beside the button that says Routing Preset. Right click on those buttons for the various options. You can also choose input options by clicking above the Pan fader in the channel strip.
I don't think it matters whether your inputs are linked (the little chain link button) or not. It's more of a visual feature.
IDK... I got mine set up pretty quickly without any trouble so I haven't had to mess with it too much.
Cheers.