Please upgrade first and try if you can reproduce the problem with the latest stable version.

I'm using winSCP scripting (from Windows schedule task) version 4.2.7 (Build 758) on Window 2003 SP2
It is running every few hours to synchronize my directory with a remote directory using SFTP protocol.
It is usually working fine, but sometimes I see the files in my directory and the file is not copied to the remote directory.
When I then ran the schedule task manually, it did copy the file
Looking at the last day's log I see some different when the file is copied to the times it is not.
I copied below the log lines related to this issue.

The scripting file content is:

# Automatically abort script on errors
option batch abort
# Disable overwrite confirmations that conflict with the previous
option confirm off
# Connect using stored session
open CON1
# Force binary mode transfer
option transfer automatic
# Syncronize //FOLDER1 to remove with delete
synchronize remote "\\ServerNm\....\Foler1" //FOLDER1 -delete
# Syncronize //FOLDER2 to remove with delete
synchronize remote "\\ServerNm\....\Foler2" //FOLDER2 -delete

# Disconnect
close
# Exit WinSCP
exit

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when the file was copied:
-----------------------------------------------------------------------------------
. 2012-06-08 08:01:01.723 Changing directory to "/FOLDER1".
. 2012-06-08 08:01:01.723 Getting real path for '/FOLDER1'
> 2012-06-08 08:01:01.739 Type: SSH_FXP_REALPATH, Size: 23, Number: 16
< 2012-06-08 08:01:01.801 Type: SSH_FXP_NAME, Size: 49, Number: 16
. 2012-06-08 08:01:01.801 Real path is '/FOLDER1'
. 2012-06-08 08:01:01.817 Trying to open directory "/FOLDER1".
> 2012-06-08 08:01:01.817 Type: SSH_FXP_LSTAT, Size: 23, Number: 263
< 2012-06-08 08:01:01.880 Type: SSH_FXP_ATTRS, Size: 21, Number: 263
. 2012-06-08 08:01:01.895 Getting current directory name.
. 2012-06-08 08:01:01.895 Startup conversation with host finished.
. 2012-06-08 08:01:01.911 Collecting synchronization list for local directory '\\ServerNm\....\Foler1\' and remote directory '//FOLDER1', mode = 0, params = 3
. 2012-06-08 08:01:01.911 Listing directory "//FOLDER1".
> 2012-06-08 08:01:01.926 Type: SSH_FXP_OPENDIR, Size: 24, Number: 523
< 2012-06-08 08:01:01.989 Type: SSH_FXP_HANDLE, Size: 10, Number: 523
> 2012-06-08 08:01:01.989 Type: SSH_FXP_READDIR, Size: 10, Number: 780
< 2012-06-08 08:01:02.051 Type: SSH_FXP_STATUS, Size: 22, Number: 780
< 2012-06-08 08:01:02.067 Status code: 1
. 2012-06-08 08:01:02.067 Listing file "//FOLDER1..".
> 2012-06-08 08:01:02.067 Type: SSH_FXP_LSTAT, Size: 27, Number: 1031
< 2012-06-08 08:01:02.145 Type: SSH_FXP_ATTRS, Size: 21, Number: 1031
> 2012-06-08 08:01:02.145 Type: SSH_FXP_CLOSE, Size: 10, Number: 1284
. 2012-06-08 08:01:02.145 Synchronizing local directory '\\ServerNm\....\Foler1\\' with remote directory '//FOLDER1', params = 3
. 2012-06-08 08:01:02.161 Copying 1 files/directories to remote directory "//FOLDER1"
. 2012-06-08 08:01:02.161 PrTime: Yes; PrRO: No; Rght: rw-r--r--; PrR: No (No); FnCs: N; RIC: 01; Resume: S (102400); CalcS: No; Mask: *.*
. 2012-06-08 08:01:02.161 TM: M; ClAr: No; CPS: 0; ExclM(No):
. 2012-06-08 08:01:02.176 AscM: *.*html; *.htm; *.txt; *.php; *.php3; *.cgi; *.c; *.cpp; *.h; *.pas; *.bas; *.tex; *.pl; .htaccess; *.xtml; *.css; *.cfg; *.ini; *.sh; *.xml
. 2012-06-08 08:01:02.192 File: "\\ServerNm\....\Foler1\RMSC_Request_20120608.txt"
. 2012-06-08 08:01:02.239 Copying "\\ServerNm\....\Foler1\RMSC_Request_20120608.txt" to remote directory started.
. 2012-06-08 08:01:02.239 Ascii transfer mode selected.
. 2012-06-08 08:01:02.255 Opening remote file.
> 2012-06-08 08:01:02.255 Type: SSH_FXP_OPEN, Size: 66, Number: 1539
< 2012-06-08 08:01:02.270 Type: SSH_FXP_STATUS, Size: 21, Number: 1284
. 2012-06-08 08:01:02.270 Discarding reserved response
< 2012-06-08 08:01:02.333 Type: SSH_FXP_HANDLE, Size: 10, Number: 1539
> 2012-06-08 08:01:02.348 Type: SSH_FXP_WRITE, Size: 4011, Number: 2054
. 2012-06-08 08:03:26.378 687 skipped SSH_FXP_WRITE, SSH_FXP_READ, SSH_FXP_DATA and SSH_FXP_STATUS packets.
> 2012-06-08 08:03:26.393 Type: SSH_FXP_CLOSE, Size: 10, Number: 90372
> 2012-06-08 08:03:26.409 Type: SSH_FXP_SETSTAT, Size: 62, Number: 1801
< 2012-06-08 08:03:26.675 Type: SSH_FXP_STATUS, Size: 21, Number: 89862
< 2012-06-08 08:03:27.565 Type: SSH_FXP_STATUS, Size: 21, Number: 90118
< 2012-06-08 08:03:27.565 Type: SSH_FXP_STATUS, Size: 21, Number: 90372
< 2012-06-08 08:03:27.581 Status code: 0
< 2012-06-08 08:03:27.581 Type: SSH_FXP_STATUS, Size: 21, Number: 1801
< 2012-06-08 08:03:27.596 Status code: 0
. 2012-06-08 08:03:27.612 Collecting synchronization list for local directory '\\ServerNm\....\Foler2' and remote directory '//FOLDER2', mode = 0, params = 3
. 201
------------------------------------------------------------------------------------
when new files don't exists:
------------------------------------------------------------------------------------

. 2012-06-07 10:15:02.468 We believe the server has signed timestamps bug
. 2012-06-07 10:15:02.468 We will use UTF-8 strings for status messages only
. 2012-06-07 10:15:02.484 Changing directory to "/FOLDER1".
. 2012-06-07 10:15:02.484 Getting real path for '/FOLDER1'
> 2012-06-07 10:15:02.484 Type: SSH_FXP_REALPATH, Size: 23, Number: 16
< 2012-06-07 10:15:02.578 Type: SSH_FXP_NAME, Size: 49, Number: 16
. 2012-06-07 10:15:02.578 Real path is '/FOLDER1'
. 2012-06-07 10:15:02.578 Trying to open directory "/FOLDER1".
> 2012-06-07 10:15:02.578 Type: SSH_FXP_LSTAT, Size: 23, Number: 263
< 2012-06-07 10:15:02.687 Type: SSH_FXP_ATTRS, Size: 21, Number: 263
. 2012-06-07 10:15:02.687 Getting current directory name.
. 2012-06-07 10:15:02.703 Startup conversation with host finished.
. 2012-06-07 10:15:02.703 Collecting synchronization list for local directory '\\ServerNm\....\Foler1' and remote directory '//FOLDER1', mode = 0, params = 3
. 2012-06-07 10:15:02.718 Listing directory "//FOLDER1".
> 2012-06-07 10:15:02.718 Type: SSH_FXP_OPENDIR, Size: 24, Number: 523
< 2012-06-07 10:15:02.796 Type: SSH_FXP_HANDLE, Size: 10, Number: 523
> 2012-06-07 10:15:02.796 Type: SSH_FXP_READDIR, Size: 10, Number: 780
< 2012-06-07 10:15:02.875 Type: SSH_FXP_STATUS, Size: 22, Number: 780
< 2012-06-07 10:15:02.875 Status code: 1
. 2012-06-07 10:15:02.875 Listing file "//FOLDER1/..".
------------------------------------------------------------------------------------
when new file exists and the file is not copied:
------------------------------------------------------------------------------------
. 2012-06-08 07:15:02.961 Changing directory to "/FOLDER1".
. 2012-06-08 07:15:02.977 Getting real path for '/FOLDER1'
> 2012-06-08 07:15:02.977 Type: SSH_FXP_REALPATH, Size: 23, Number: 16
< 2012-06-08 07:15:03.055 Type: SSH_FXP_NAME, Size: 49, Number: 16
. 2012-06-08 07:15:03.055 Real path is '/FOLDER1'
. 2012-06-08 07:15:03.070 Trying to open directory "/FOLDER1".
> 2012-06-08 07:15:03.070 Type: SSH_FXP_LSTAT, Size: 23, Number: 263
< 2012-06-08 07:15:03.133 Type: SSH_FXP_ATTRS, Size: 21, Number: 263
. 2012-06-08 07:15:03.148 Getting current directory name.
. 2012-06-08 07:15:03.148 Startup conversation with host finished.
. 2012-06-08 07:15:03.180 Closing connection.
. 2012-06-08 07:15:03.180 Sending special code: 12
. 2012-06-08 07:15:03.180 Sent EOF message