The time-stamps used by CmdSync are the last modified dates and times which are maintained by the operating system for each file stored on disk.
Fat file systems, as used by Windows 95, can only store time-stamps to the nearest 2 seconds and this can cause problems when comparing with files stored on an NTFS file system as used by Windows NT4, which maintains time-stamps to an accuracy of milli-seconds.
To handle this problem use the Ignore two second time differences option.