I have encountered this same issue. I am sending large files via TCP during an HTTP session and I see packets being transmitted out of order. This is unacceptable. Attached is a copy for a Wireshark capture of communications between the CC3000 (192.168.1.101) and my PC web browser (192.168.1.102). The HTTP server will transmit segments of the file in block sizes determined by the lesser of the following (1000 bytes or the remaining bytes to be transmitted from the file). I have instrumented my code an have observed that the send() function was indeed sent a series of 1000 bytes blocks followed by the last segment of 355 bytes. However, as can be seen from the Wireshark trace, these are being transmitted out of order by the CC3000.
I changed the code to wait for a HCI_EVENT_CC3000_CAN_SHUT_DOWN event after each send. This appeared to "fix" the problem, but at a HUGE performance hit to data throughput. The issue seems to be triggered by numerous back-to-back send() requests from the application code.
This is serious enough to scrap further development with your part. Please get back to me with the corrective action ASAP.