DawnG, your log shows only 1 file transfer,
Code:
[09:01:59] [R] STOR favicon.ico
[09:01:59] [R] 150 Accepted data connection
[09:01:59] [R] 226-File successfully transferred
[09:01:59] [R] 226 0.091 seconds (measured here), 3.43 Kbytes per second
[09:01:59] Upload: favicon.ico 318 bytes in 0.09 second (0.3 KB/s)
and it uploaded correctly..
Please provide session logs when you actually encounter your problem. And please make sure that timestamps like above are turned on. Timing of commands is important to figure out what's going on.