Edward,
To answer your questions:
1) I do not see this being an issue, the code on the CC3000 EEPROM should be agnostic to the host processor being used. Can you confirm that you flashed your CC3000 module in the correct order (driver, then firmware) and saw the correct LEDs light up after each step?
2) When you set the CC3000 to auto-connect using wlan_ioctl_set_connection_policy (1,0,0), you will not be using any profile that smartconfig has created.
How to use SmartConfig:
Before running SmartConfig, you should have the connection policy reset using wlan_ioctl_set_connection_policy (0,0,0). Once SmartConfig is run, it will automatically set-up a profile for you. Next, set your policy to use profiles by using wlan_ioctl_set_connection_policy (0,0,1), then reset the CC3000 using wlan_stop() then wlan_start().
If you are trying to switch between policies (i.e. switch from Auto Connect to using profiles) you must reset the CC3000. From the wiki link I posted earlier: "The device must be reset before a policy can be applied. Profiles must first be added to the CC3000 device before they can be used."
Hope that helps,
Keegan