Back when I had the CC3000 connected to the MSP430 board, I did have some problems connecting, but I didn't have the logic analyzer connected so I can't say for certain that it was the same thing. If it comes down to it I'll see if I can put the CC3000 back on the MSP430 board to verify it's the same problem.
The event is never being sent by the CC3000. It's pretty clear looking at the logic analyzer trace. I expect the following sequence when turning on the CC3000 and then doing a wlan_connect():
cmd HCI_CMND_SIMPLE_LINK_START 0x4000
evt HCI_CMND_SIMPLE_LINK_START 0x4000
cmd HCI_CMND_READ_BUFFER_SIZE 0x400B
evt HCI_CMND_READ_BUFFER_SIZE 0x400B
cmd HCI_CMND_EVENT_MASK 0x0008
evt HCI_CMND_EVENT_MASK 0x0008
cmd HCI_CMND_WLAN_CONNECT 0x0001
evt HCI_CMND_WLAN_CONNECT 0x0001
evt HCI_EVNT_WLAN_UNSOL_CONNECT 0x8001
evt HCI_EVNT_WLAN_UNSOL_DHCP 0x8010
The SPI sequences for the "cmd" lines are initiated by the microcontroller asserting the CS line (except the first 'start' one which is special). The SPI sequences for the "evt" lines are initiated by the CC3000 asserting the IRQ line.
When the issue shows up, the last two events never occur, evident by the IRQ line never being asserted by the CC3000 after the 0x0001 event. I didn't log in to the AP to see if the CC3000 was actually connected, but it doesn't really matter if the CC3000 never reports that it got connected. I did read the connection status from the CC3000 and it showed that it was disconnected.