Reported at issue 11228 - I can confirm the problem exists with DNN 5.2.

I also suggested a fix in a different forum post:

  ALTER VIEW dbo.{objectQualifier}vw_Tabs
  AS
    SELECT    
        T.TabID,
        T.TabOrder,
        T.PortalID,
        T.TabName,
        T.IsVisible,
        T.ParentId,
        T.[Level],
        CASE WHEN I.FileID IS NULL THEN T.IconFile
             ELSE '~/' + P.HomeDirectory + '/' + I.Folder + I.FileName
        END AS IconFile,
        CASE WHEN L.FileID IS NULL THEN T.IconFileLarge
             ELSE '~/' + P.HomeDirectory + '/' + L.Folder + L.FileName
        END AS IconFileLarge,
        T.DisableLink,
        T.Title,
        T.Description,
        T.KeyWords,
        T.IsDeleted,
        T.SkinSrc,
        T.ContainerSrc,
        T.TabPath,
        T.StartDate,
        T.EndDate,
        T.Url,
        CASE WHEN EXISTS (SELECT  1 FROM dbo.Tabs T2 WHERE T2.ParentId = T.TabId) THEN 'true' ELSE 'false' END AS HasChildren,
        T.RefreshInterval,
        T.PageHeadText,
        T.IsSecure,
        T.PermanentRedirect,
        T.SiteMapPriority,
        T.CreatedByUserID,
        T.CreatedOnDate,
        T.LastModifiedByUserID,
        T.LastModifiedOnDate
    FROM dbo.{objectQualifier}Tabs AS T
        LEFT JOIN dbo.{objectQualifier}Portals AS P ON P.PortalID = T.PortalID
        LEFT JOIN dbo.{objectQualifier}Files AS I ON I.FileID = CASE WHEN LEFT(LOWER(T.IconFile), 7) = 'fileid=' THEN CAST((RIGHT(LOWER(T.IconFile), LEN(T.IconFile) - 7)) AS int) ELSE -1 END
        LEFT JOIN dbo.{objectQualifier}Files AS L ON L.FileID = CASE WHEN LEFT(LOWER(T.IconFileLarge), 7) = 'fileid=' THEN CAST((RIGHT(LOWER(T.IconFileLarge), LEN(T.IconFileLarge) - 7)) AS int) ELSE -1 END

file manager does not display /images folder, only associated /portals subfolder.

In DNN 5.1+ above the file selector, there is an option group to specify appropriate location.

Synchronize files didn't do the job for me with DNN 5.4.0 - the problem still exists for non-root portals.

DNN 5.4 has a new view definition, so you'll need to use the updated script below:

ALTER VIEW {databaseOwner}{objectQualifier}vw_Tabs
AS
    SELECT    
        T.TabID,
        T.TabOrder,
        T.PortalID,
        T.TabName,
        T.IsVisible,
        T.ParentId,
        T.[Level],
        CASE WHEN I.FileID IS NULL THEN T.IconFile
             ELSE '~/' + P.HomeDirectory + '/' + I.Folder + I.FileName
        END AS IconFile,
        CASE WHEN L.FileID IS NULL THEN T.IconFileLarge
             ELSE '~/' + P.HomeDirectory + '/' + L.Folder + L.FileName
        END AS IconFileLarge,
        T.DisableLink,
        T.Title,
        T.Description,
        T.KeyWords,
        T.IsDeleted,
        T.SkinSrc,
        T.ContainerSrc,
        T.TabPath,
        T.StartDate,
        T.EndDate,
        T.Url,
        CASE WHEN EXISTS (SELECT  1 FROM {databaseOwner}{objectQualifier}Tabs T2 WHERE T2.ParentId = T.TabId) THEN 'true' ELSE 'false' END AS HasChildren,
        T.RefreshInterval,
        T.PageHeadText,
        T.IsSecure,
        T.PermanentRedirect,
        T.SiteMapPriority,
        CI.ContentItemID,
        CI.Content,
        CI.ContentTypeID,
        CI.ModuleID,
        CI.ContentKey,
        CI.Indexed,
        T.CreatedByUserID,
        T.CreatedOnDate,
        T.LastModifiedByUserID,
        T.LastModifiedOnDate
    FROM {databaseOwner}{objectQualifier}Tabs AS T
        LEFT OUTER JOIN  {databaseOwner}{objectQualifier}ContentItems AS CI ON T.ContentItemID = CI.ContentItemID
        LEFT JOIN {databaseOwner}{objectQualifier}Portals AS P ON P.PortalID = T.PortalID
        LEFT JOIN {databaseOwner}{objectQualifier}Files AS I ON I.FileID = CASE WHEN LEFT(LOWER(T.IconFile), 7) = 'fileid=' THEN CAST((RIGHT(LOWER(T.IconFile), LEN(T.IconFile) - 7)) AS int) ELSE -1 END
        LEFT JOIN {databaseOwner}{objectQualifier}Files AS L ON L.FileID = CASE WHEN LEFT(LOWER(T.IconFileLarge), 7) = 'fileid=' THEN CAST((RIGHT(LOWER(T.IconFileLarge), LEN(T.IconFileLarge) - 7)) AS int) ELSE -1 END
GO