Hi Jonathan,
1. Please send us a logger file according to these instructions:
http://processors.wiki.ti.com/index.php/CC3000_Logger
It will help us understand what is happening from the CC3000 device side.
2. Please set the SPI clock to 1Mhz. According to your scope shot it looks like ~140Khz.
3. Please try to start the device with wlan_start(1) instead of wlan_start(0), just to eliminate damaged patches in the EEPROM.
Yael