Please ensure the following:
1. Files are placed in a sub-folder under "Shared" or "Private".
2. Only an administrator has rights to create a folder directly under the "Shared" folder. In case, you are a non-admin user on Egnyte, please ensure that the files are placed in a sub-folder under "Shared" that has synchronized down to the Desktop Sync. Also ensure that you have "Read/Write" permissions to the folder by logging into the Egnyte account from the web interface (browser). If you are not allowed to upload files from the browser into the same folder, then you may be having "Read only" access to the folder.
2. In case of "Private" folders, even an administrator cannot manually create a sub-folder. The folders under "Private" are the private folders of Egnyte Power users and these folders will have the name of their respective Egnyte username. These get synchronized down if you have configured to sync the Private folder.
If files are still getting skipped then please click on 'Contact Support' located on the top right hand corner of the Desktop Sync Settings page at http://127.0.0.1:8806. Leave the 'Send Logs' box checked. We will review the logs to see what is causing the issue.