Here is the modified log file for this problem. It doesn't tell much more, I'm still not sure how to fix this.
. 2009-09-16 15:07:27.687 --------------------------------------------------------------------------
. 2009-09-16 15:07:27.687 WinSCP Version 4.1.9 (Build 416) (OS 5.1.2600 Service Pack 3)
. 2009-09-16 15:07:27.687 Login time: Wednesday, September 16, 2009 3:07:27 PM
. 2009-09-16 15:07:27.687 --------------------------------------------------------------------------
. 2009-09-16 15:07:27.687 Session name: [SESSION INFO]
. 2009-09-16 15:07:27.687 Host name: [HOST INFO] (Port: 21)
. 2009-09-16 15:07:27.687 User name: [USER NAME] (Password: Yes, Key file: No)
. 2009-09-16 15:07:27.703 Tunnel: No
. 2009-09-16 15:07:27.703 Transfer Protocol: FTP
. 2009-09-16 15:07:27.703 Ping type: C, Ping interval: 30 sec; Timeout: 15 sec
. 2009-09-16 15:07:27.703 Proxy: none
. 2009-09-16 15:07:27.703 FTP: Passive: No
. 2009-09-16 15:07:27.703 Local directory: default, Remote directory: home, Update: No, Cache: Yes
. 2009-09-16 15:07:27.703 Cache directory changes: Yes, Permanent: Yes
. 2009-09-16 15:07:27.703 DST mode: 1
. 2009-09-16 15:07:27.703 --------------------------------------------------------------------------
. 2009-09-16 15:07:27.859 Connecting to [DOMAIN NAME] ...
. 2009-09-16 15:07:27.875 Connected with [DOMAIN NAME]. Waiting for welcome message...
< 2009-09-16 15:07:27.906 220-FileZilla Server version 0.9.32 beta
< 2009-09-16 15:07:27.906 220-written by Tim Kosse (Tim.Kosse@gmx.de)
< 2009-09-16 15:07:27.906 220 Please visit
http://sourceforge.net/projects/filezilla/
> 2009-09-16 15:07:27.906 USER [USER NAME]
< 2009-09-16 15:07:27.921 331 Password required for [USER NAME]
> 2009-09-16 15:07:27.921 PASS ******
< 2009-09-16 15:07:27.937 230 Logged on
> 2009-09-16 15:07:27.937 SYST
< 2009-09-16 15:07:27.953 215 UNIX emulated by FileZilla
> 2009-09-16 15:07:27.953 FEAT
< 2009-09-16 15:07:27.968 211-Features:
< 2009-09-16 15:07:27.968 MDTM
< 2009-09-16 15:07:27.968 REST STREAM
< 2009-09-16 15:07:27.968 SIZE
< 2009-09-16 15:07:27.968 MLST type*;size*;modify*;
< 2009-09-16 15:07:27.968 MLSD
< 2009-09-16 15:07:27.968 UTF8
< 2009-09-16 15:07:27.968 CLNT
< 2009-09-16 15:07:27.968 MFMT
< 2009-09-16 15:07:27.968 211 End
. 2009-09-16 15:07:27.968 Connected
. 2009-09-16 15:07:27.968 --------------------------------------------------------------------------
. 2009-09-16 15:07:27.968 Using FTP protocol.
. 2009-09-16 15:07:27.968 Doing startup conversation with host.
> 2009-09-16 15:07:27.968 PWD
< 2009-09-16 15:07:27.984 257 "/" is current directory.
. 2009-09-16 15:07:27.984 Getting current directory name.
. 2009-09-16 15:07:27.984 Startup conversation with host finished.
. 2009-09-16 15:07:27.984 Copying 1 files/directories to remote directory "/"
. 2009-09-16 15:07:27.984 PrTime: Yes; PrRO: No; Rght: rw-r--r--; PrR: No (No); FnCs: N; RIC: 01; Resume: S (102400); CalcS: No; Mask:
. 2009-09-16 15:07:27.984 TM: M; ClAr: No; CPS: 0; ExclM(No):
. 2009-09-16 15:07:27.984 AscM: *.*html; *.htm; *.txt; *.php; *.php3; *.cgi; *.c; *.cpp; *.h; *.pas; *.bas; *.tex; *.pl; .htaccess; *.xtml; *.css; *.cfg; *.ini; *.sh; *.xml
. 2009-09-16 15:07:27.984 File: "C:\Documents and Settings\Rockwall3.WS6A\My Documents\My ScanSnap\ScanSnap_FTP\2009_09_16_14_32_55.pdf"
. 2009-09-16 15:07:27.984 Copying "C:\Documents and Settings\Rockwall3.WS6A\My Documents\My ScanSnap\ScanSnap_FTP\2009_09_16_14_32_55.pdf" to remote directory started.
. 2009-09-16 15:07:27.984 Binary transfer mode selected.
. 2009-09-16 15:07:27.984 Starting upload of C:\Documents and Settings\Rockwall3.WS6A\My Documents\My ScanSnap\ScanSnap_FTP\2009_09_16_14_32_55.pdf
> 2009-09-16 15:07:27.984 TYPE A
< 2009-09-16 15:07:28.000 200 Type set to A
> 2009-09-16 15:07:28.000 PORT 10,10,2,80,13,150
< 2009-09-16 15:07:28.015 200 Port command successful
> 2009-09-16 15:07:28.015 LIST
< 2009-09-16 15:07:28.031 150 Opening data channel for directory list.
< 2009-09-16 15:07:28.062 226 Transfer OK
> 2009-09-16 15:07:28.078 TYPE I
< 2009-09-16 15:07:28.093 200 Type set to I
> 2009-09-16 15:07:28.093 PORT 10,10,2,80,13,152
< 2009-09-16 15:07:28.109 200 Port command successful
> 2009-09-16 15:07:28.109 STOR 2009_09_16_14_32_55.pdf
< 2009-09-16 15:07:28.125 150 Opening data channel for file transfer.
< 2009-09-16 15:07:28.125 425 Can't open data connection.
. 2009-09-16 15:07:28.125 Copying files to remote side failed.
* 2009-09-16 15:07:28.125 (ExtException) Copying files to remote side failed.
* 2009-09-16 15:07:28.125 Can't open data connection.
. 2009-09-16 15:07:28.125 Asking user:
. 2009-09-16 15:07:28.125 Error transferring file 'C:\Documents and Settings\Rockwall3.WS6A\My Documents\My ScanSnap\ScanSnap_FTP\2009_09_16_14_32_55.pdf'. ("Copying files to remote side failed.","Can't open data connection.")
* 2009-09-16 15:07:28.125 (EScpSkipFile) Error transferring file 'C:\Documents and Settings\Rockwall3.WS6A\My Documents\My ScanSnap\ScanSnap_FTP\2009_09_16_14_32_55.pdf'.
* 2009-09-16 15:07:28.125 Copying files to remote side failed.
* 2009-09-16 15:07:28.125 Can't open data connection.
. 2009-09-16 15:07:36.484 Disconnected from server