Thanks for your report. I'll check it.
Yes it makes me crazy. WinSCP standalone and as plugin ignores the difference of one second, because FAT/FAT32 uses even second rounded up timestamps only. This is fine for NTFS <> FAT(32). But last time I found that Netware uses even seconds too, but rounded down to even seconds. What they think, want to be faster!?
So it will be very fine, to let us configure the maximum of difference in seconds.