If the source, or destination, is set to use a DFS share, e.g. \\servername\DFS\, then it may not find any sub-folders in the share. This is due to the way DFS works. Each sub-folder is actually a junction point and not a standard folder. By default SyncBack will ignore junction points.
To stop SyncBack from ignoring junction points: modify the profile, switch to Expert mode, go to Compare Options > Attributes page and untick the option Ignore NTFS junction points (reparse points).