I came to the forum to report the same problem. I copied a few files from my Windows 2000 machine to my linux box and it showed the same date/time as windows for teh file, but when I read the file date/time with my application some files were one hour off (some files were one hour young then the windows ones). I then tried another tool, the SSH client from www.ssh.com and it showed me the "wrong" date/time I am getting with my application. So I copied the files with the SSH tool and the date was the same as on windows and my application also gave me the windows date/time so they matched.
It seems like WinSCP is copying the files, modifying the date stamp and showing a wrong one (although it would be "right", if it wouldn' the wrong one).
When working with files, WinSCP attempt to apply DST on the timestamp. You may modify the behaviour on Environment tab of Login window.
Also note that the time you get from Windows (NT-based at least) does not include timezone or DST shift. Windows explorer also shows different time than actually stored in the filesystem.