The WinXP disk uses NTFS.
As a test, I copied the suspect file into a test directory on the Windows machine, created a test directory on the Mac machine (on the FAT32 drive), and copied the file over with WinSCP. I then used the Cygwin tool "touch" to update the time of the local file to "now", and then repeatedly tried synchronizing with WinSCP. After a "touch", of course WinSCP would declare the files different and copy the local file to the remote, ending up with the remote file the same as the remote. However, if I'd happened to "touch" the local file so that its last digit was odd then a repeated synchronize would show it again, and again, and again; an even last digit would only need to be synchronized once.
On my most recent try, the local timestamp given by WinSCP is 6/6/2008 1:22:35PM; the remote timestamp is 6/6/2008 1:22;34PM.
There's something else weird going on. As I've said, in WinSCP the local and remote files all have the same time stamps, except for those mysterious files where the local seconds are odd and the remote seconds are even. And, the WinSCP time stamp for the local file matches that given by both Windows and the Cygwin command-line tools. However, looking on the Mac (both with command line tools and the Finder), the time on the remote file is one hour earlier than shown in the WinSCP remote pane. (Both machines are set to EDT.)
Is there anything else you'd like me to look at?
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