When files are uploaded using FTP, they receive the date and time of the FTP server. Auto FTP Manager uses the FTP's MDTM command to set the file's correct date and time after accounting for Time Zone Difference.
According to the standards, the MDTM command should get the modification date and time (and not set it). However, many FTP servers like WS_FTP support this useful extension.
Windows Server 2003 has a basic FTP server that does not support this extension for the MDTM command. As a result, the uploaded files always get the date and time of the FTP server. Thus, synchronization based on date does not work.
We have planned an approach to date-based synchronization that will eliminate Auto FTP Manager's need to rely on the MDTM command. We will include this in one of our future releases.