The problem I'm encountering, which may be what the OP is describing, is a bug I believe and not just a simple difference between Windows and *nix.
If I sign in via SSH and look at the timestamps, they are correct. That is, one hour behind me, since that's where the hosting server is located. If I view the files in WinSCP, the time is off by 2 hours, showing as an hour ahead of me. I believe that somehow, WinSCP is trying to compensate for DST but doing it backwards (adding when it should be subtracting) or it's trying to adjust the servers file times but is overdoing it.
Either way, it's not a simple one hour difference, it's a two hour difference. I should point out that these are files that are created on and updated on the hosting server, not files being transferred via WinSCP. I know that if I look at my hosting server and see a time that is one hour behind me, that it's correct because of its location. But I find it hard to believe that an offset of two hours is being blamed on Windows -vs- *nix.
Please address this minor issue, as it is rather confusing.