Try clicking the import button and point the import dialog window to that folder. Then click on All Photos at the top. Do these supposedly missing images show in the grid view section and if they do are they grayed out?
Just tried that, but all the photos are greyed out on the import dialog. So I can't actually tell which photos are missing. Any ideas?
The name of the files are displayed under the images in the Import dialog. Do a cross reference for one of the supposedly missing images to see if it shows up in the import dialog. More than likely they are already in the LR catalog and that is why the Sync feature isn't picking them up or the ones missing aren't really image files.
If the photos are greyed out, this means that photos have been previously imported into Lightroom, and you cannot and should not import them a second time.
You need to find the photos in Lightroom. Click on All Photographs, turn off filters, and then search for one of the photos by file name to find it.
In this case, Synchronize and Import seem to be working as they were designed to work.