I have this problem too.
Logo and media files disappear.
'You do not have permission to see files' in site settings and media modules
Can reset permissions in Filemanager, but recursivity not perfect, may have to set inner folder separately.
Then must set each image to view - default image s first in the list, not the original.
Scheduled File synchronisation function wipes out access to root and lower folders, so have disabled. Position stabilised but not cured.
SQL folderpermissions - entries wiped out when sheduled task runs.
Do get sheduled sync task throwing exeception ' Invalid Path Id' . I think this is what causes the folders to lose their 'permissions' as the task does not complete.
Elsewhere there is a reference to 'capitalisation, lowered' problems in later DNN versions.
Do have file names with space, -, _, capitals, mixed case names
Folders seem OK , consistently like \Image (not \image)
If we can trace the sheduled file sync exception I think we will have an answer........
DotNetNuke.Services.FileSystem.SynchronizeFileSystem, DOTNETNUKE
File System Synchronization failed. System.ArgumentException: The path is not of a legal form. at System.IO.Path.NormalizePathFast(String path, Boolean fullCheck) at System.IO.Path.GetFullPathInternal(String path) at System.IO.DirectoryInfo..ctor(String path) 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()