Exactly the same thing happened to me - it fails at exactly the same point:
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Got smart config data
Timed out waiting to connect
I.e. it clearly appears to receive the Smart Config data but then fails to be able to use it to connect.
The module still works fine and successfully connects to the network if I don't use Smart Config and instead hard code the SSID and password in my sketch.
I wasn't actually changing things about with my Arduino/CC3000 setup when things first went wrong - it just stopped working one day.
As I'm using the breakout board connected up via a breadboard, rather than the shield version, I assumed one of my wires had come loose (though this seemed less likely later when I could prove to myself that everything worked if I used the non-Smart Config approach).
I checked all my wiring and actually pulled everything out and rewired it - however as pointed out the fact that it works with the hardcoded SSID and password approach makes me think it's not a wiring problem. And the fact that it seems to be able to receive the Smart Config data suggests there isn't an issue with being able to monitor wifi channels.
So why making a connection with the received data should timeout I don't know.