I'm having the exact same problem and it's making me wanna put all my stuff in a pile, set it ablaze, and jump on top. I'm working with a focusrite 4i4, with an xlr mic and ts 1/4" from a yamaha keyboard in the respective #1 and #2 analogue ports on front. I run the interface through a powered usb hub, and the hub connects to the pad through a camera connector cable. I thought I'd gotten a bead on it, as it seemed to happen most often when i had both ports active, AKA it would record just the piano or the mic happily enough, just not both together for some reason. But then I've since had problems with just the mic plugged in as well. Sometimes it shows gray and muted, other times just gray, either way it's *extremely* frustrating.
As with the OP, i've looked at (for instance) switcher studio, which can manage it all just fine, but i'd like to avoid paying an extra $30 - $50 a month because of a grayed out audio signal in an otherwise (normally) very functional app.