Here's the tail end of the log...
What I note here is that TransferSocket.cpp(1179): Close() is called 3 times, the last being from the ~CTransferSocket(). I'd suspect the 'timeout' is because you are trying to close a connection in the destructor that you have already closed (twice).
. 2008-07-03 13:17:31.245 Session upkeep
. 2008-07-03 13:17:31.964 Session upkeep
. 2008-07-03 13:17:32.323 Session upkeep
. 2008-07-03 13:17:32.902 Session upkeep
. 2008-07-03 13:17:33.464 Session upkeep
. 2008-07-03 13:17:33.745 Session upkeep
. 2008-07-03 13:17:34.324 Session upkeep
. 2008-07-03 13:17:34.324 TransferSocket.cpp(557): OnClose(0) caller=0x01d844a4
. 2008-07-03 13:17:34.324 TransferSocket.cpp(1179): Close() caller=0x01d844a4
. 2008-07-03 13:17:34.324 TransferSocket.cpp(1179): Close() caller=0x01d844a4
. 2008-07-03 13:17:34.324 FtpControlSocket.cpp(2070): TransferEnd(24) OpMode=24 OpState=19 caller=0x01d48204
. 2008-07-03 13:17:34.324 FtpControlSocket.cpp(2107): FileTransfer(0, TRUE, 0) OpMode=24 OpState=19 caller=0x01d48204
. 2008-07-03 13:17:34.324 TransferSocket.cpp(108): ~CTransferSocket() caller=0x01d844a4
. 2008-07-03 13:17:34.324 TransferSocket.cpp(1179): Close() caller=0x01d844a4
. 2008-07-03 13:17:49.027 Timeout detected.
. 2008-07-03 13:17:49.027 FtpControlSocket.cpp(1199): DoClose(0) OpMode=24 OpState=19 caller=0x01d48204
. 2008-07-03 13:17:49.027 FtpControlSocket.cpp(4184): ResetOperation(4100) OpMode=24 OpState=19 caller=0x01d48204
. 2008-07-03 13:17:49.043 Copying files from remote side failed.
. 2008-07-03 13:17:49.043 Got reply 1004 to the command 4
. 2008-07-03 13:17:49.043 Connection was lost, asking what to do.
. 2008-07-03 13:17:49.043 Asking user:
. 2008-07-03 13:17:49.043 Lost connection. ("Timeout detected.","Copying files from remote side failed.","Downloading in BINARY file MyFileName.exe (214426659)")
* 2008-07-03 13:17:50.746 (ESshFatal) Lost connection.
* 2008-07-03 13:17:50.746 Timeout detected.
* 2008-07-03 13:17:50.746 Copying files from remote side failed.
* 2008-07-03 13:17:50.746 Downloading in BINARY file MyFileName.exe (214426659)
* 2008-07-03 13:17:50.746 Copying files from remote side failed.
. 2008-07-03 13:17:53.933 FtpControlSocket.cpp(181): ~CFtpControlSocket() caller=0x01d48204
. 2008-07-03 13:17:53.933 FtpControlSocket.cpp(1199): DoClose(0) OpMode=0 OpState=-1 caller=0x01d48204
. 2008-07-03 13:17:53.933 FtpControlSocket.cpp(4184): ResetOperation(4100) OpMode=0 OpState=-1 caller=0x01d48204
. 2008-07-03 13:17:53.933 ControlSocket.cpp(89): ~CControlSocket() caller=0x01d48204