If there is one hour time difference on some files, it is probably caused by different treatment of DST in different systems/applications. You can use "timestamp synchronization" function of WinSCP to align the timestamps.
First I've been using winscp3 for some time now and I'm very happy with it, and I hope that my question is not too obvious.
I am using winscp 3.74 on windows XP with the lastest updates.
I use winscp to synchronize between XP (ntfs) and two linux workstations (ext3). Recently some error deleted one of my "synchronized" directories and I thought it would be faster to copy the files onto an external fat32 drive, and then use that drive to copy the files to my windows machine by physically moving the drive. I did that, and then set to be certain that my manual synchronization worked correctly. What I found was that winscp decided that many files in no obvious pattern needed to be resynchronized even though the new files should have been direct copies of what I was syncing to.
If anyone can help me understand this so I can better manage my backup process I would appreciate it.