MacOS – Caps Lock key mapped to a second Control key, reset after wake in Mountain Lion

While I believe Macbooks Air did this before Mountain Lion, you seem to be experiencing a resume from standby. All Mac laptops, by default, write the contents of memory to disk when they sleep, but leave the power to the RAM on for a quick resume. Writing the contents of memory to the disk occurs so that you won't lose data if the system loses power.

However, on Macbooks Air and Retina Macbooks Pro, which have built-in Flash memory (which Apple distinguishes from 2.5" SSDs on Macbooks Pro), in order to advertise a 30-day standby time, after an hour the system removes power from the RAM. So, if you leave it asleep for more than an hour, you'll actually be resuming from the disk. It's a lot faster than on a device without an SSD, but it's still a noticeable delay. Apple calls this "standby", and while it's resuming you basically see a still image of the login screen that you can't interact with.

You can disable standby with this unsupported command: sudo pmset -a standby 0. This will cause your battery to drain much more when you leave the system asleep, but it'll make it resume much more quickly.

Apple's documentation on standby mode is here.

Siracusa's review mentions this behavior, and it's been evolving since Snow Leopard:

DarkWake has actually been around since Snow Leopard, where it was used to periodically send out a network tickler to ensure that a sleeping Mac doesn't lose its DHCP lease. In Lion, plugging in or unplugging a USB device could briefly put a Mac into DarkWake to reconfigure the peripheral bus before going back to sleep. Mountain Lion does all of the above while also carving out some time to get real work done while the master is away.

DarkWake is the state the system is in when Power Nap is running. In Lion, it would enter DarkWake to deal with processing the USB connection, then it would go back to sleep. In Mountain Lion, when a USB device is connected, the Mac enters DarkWake to deal with processing the USB connection and also uses this state to do the various Power Nap tasks.