I'm getting a very similar error in schedule file sync. Except it oocurs in RemoveOrphanedFolders. Seems to be because the returned PhysicalPath is incorrect, presumably beause of the call to PortalSettings as described above. Was this ever resolved. I have the problem in 4.3.7 (& 3.3.7). Trace below:-
Message: System.NullReferenceException: Object reference not set to an instance of an object. at DotNetNuke.Entities.Portals.PortalController.GetCurrentPortalSettings() at DotNetNuke.Services.FileSystem.FolderInfo.get_PhysicalPath() at DotNetNuke.Common.Utilities.FileSystemUtils.RemoveOrphanedFolders(Int32 PortalId) at DotNetNuke.Common.Utilities.FileSystemUtils.SynchronizeFolder(Int32 PortalId, String physicalPath, String relativePath, Boolean isRecursive, Boolean syncFiles, Boolean forceFolderSync) at DotNetNuke.Services.FileSystem.SynchronizeFileSystem.Synchronize() at DotNetNuke.Services.FileSystem.SynchronizeFileSystem.DoWork()