Microsoft introduced a number of junction points in Windows Vista. Briefly, a junction point is a link to another folder. Another way to think of it is as an alias. The following article has details:

The purpose of creating these junction points was to provide backwards compatibility with programs that certain expected folders to exist. Microsoft recommends that junction points should be skipped by backup software and not copied, which is what SyncBack does by default.

Because those junction points are skipped it may appear some files and folders are not being copied. This is an incorrect assumption. It is merely the junction points themselves which are not being copied. A junction point contains no data or files and is simply a link to a real folder containing the actual files.

By default SyncBack will ignore all junction points. However, with V11, you can configure it to just ignore backwards compatibility junction points or even copy and remap them: modify your profile, enable Expert mode, go to Copy/Delete > Links.

In V10, to SyncBack follow junction points: modify your profile, enable Expert mode, go to the Compare Options > Attributes settings page, and untick the checkbox "Ignore NTFS junction points".

For reference, Windows has the following junction points:

Windows Vista Junction Points
Old PathNew Path
\Documents and Settings\Users
\Documents and Settings\Default User or
\Users\Default or
\Documents and Settings\<user>\My Documents\Users\<user>\Documents
\Documents and Settings\<user>\My Documents\My Pictures\Users\<user>\Pictures
\Documents and Settings\<user>\My Documents\My Music\Users\<user>\Music
\Documents and Settings\<user>\Favorites\Users\<user>\Favorites
\Documents and Settings\<user>\Application Data\Users\<user>\AppData\Roaming
\Documents and Settings\<user>\Local Settings\Application Data\Users\<user>\AppData\Local
\Documents and Settings\<user>\Start Menu\Users\<user>\AppData\Roaming\Microsoft\Windows\ Start Menu
\Documents and Settings\All Users\Users\Public
\Documents and Settings\All Users\Start Menu\ProgramData\Microsoft\Windows\Start Menu
\Documents and Settings\All Users\Desktop\Users\Public\Desktop
\ProgramData\Application Data\ProgramData
\ProgramData\Start Menu\ProgramData\Microsoft\Windows\Start Menu