This can occur if FTP is used to upload entire folders to an existing folder. Most FTP clients first delete the original folder, then re-upload an entire new folder of the same name. When this occurs, any custom permissions on the replaced folder are lost.
Instead, the replaced folder will inherit the permission settings from the parent folder. Typically this means that the folder becomes read-only and is accessible for public browsing.
If using custom permissions, it is best to upload file-by-file to ensure the custom permissions stay set.
When using FTP, this can also occur on some folders with non-standard settings such as the FrontPage "_vti..." folders, /database and others.
If you lose custom permissions on a folder, a support request must be submitted via the Alentus Support Center to have them re-applied. For the re-application of permissions, Submit a Ticket to the Technical Support Department and be sure to include the correct folder name and permission settings, in the Message Details.