Why do some files seem to change on each sync?

The default overwrite policy is “Overwrite if timestamp or size is different”. This option can be changed in the sync settings Destination tab. Most volumes work out of the box with this default setting, but some volume formats may cause files that have not been modified between syncs to be listed again in the confirmation window. For example, volumes that use the FAT file format (which is primarily used by older devices) don’t seem to support custom modification dates for directories, even though there’s no official documentation on this behaviour. It seems that whenever a directory is created, the current date is automatically set and cannot be changed. Hence SyncTime will find that the modification date of a source directory is always different from the one on the destination, trying to sync it each time. A workaround is to use the “Overwrite if source file is newer” overwrite policy instead. Beware that when using this overwrite policy, if you replace a source file with another version that has an older modification date, this change won’t be synced until you open and modify the source file so that its modification date is updated.

When you sync to another computer, such as a network attached storage (NAS), it can happen that the modification date of a copied file is reset by the destination operating system, which may cause subsequent syncs to report that the file still needs to be synced. In some cases, the problem can be solved by making sure that the network volume has both SMB and AFP services enabled and it is mounted with the same username as the account that you’re currently using on your Mac.

If you’re unsure why a file is listed in the confirmation window, select the source and destination files in the Finder, then in the main menu select File > Get Info (or press Command-I). In the Info panel you can compare the file size and modification date, at least one of which should be different between the source and destination files.