1) your Differences window display filters are not listing everything it found because it has been configured to suppress listing certain categories. Check the Help for how to configure these options.
2) The profile is Ignoring many of your files because it has been told to (filters, limits, de/selections, attributes, junction points...). The additional options (x 2)
Modify -> Log -> 'Log the reason why files/folders on [side] are ignored/skipped'
may help. Make sure the option 'Do not log skipped...' is not selected. Run a Simulated Run with these options enabled, then check the extra Ignored section (if there is one) of the log generated at the end. Note that this will not increase the number of files listed in the Differences window (Ignored files do not count as 'differences') so you need to complete a run to see the extra (if any) Ignored information in the log.
3) The profile is not being told about all subfolders\files by the device/resource in question (that is, the resource is not listing everything). The likelihood of this varies depending on the device type and file-system, which would be helpful if you checked/confirmed here.
4) Some of the files already exist/match on the other side, so are not listed in the Differences window (the window name is a clue

If you need to respond, please supply the details of the Source (see above) and your SB version (x.x.x.x, as displayed on Taskbar button and program title-bar) and Windows version. Note also that quoting the 'TB' or 'GB' doesn't always give the full picture. It often helps if you also quote 'number of files'.
Statistics: Posted by cliffhanger — Sun Jan 25, 2015 3:04 pm