Files missing in scanned folder

Hi folks. For about 2-3 months ago I got some strange issues with my XBMC movie folder. Everything was working fine until one day I couldn't watch one movie and when I browsed my files in XBMC I found several folders empty. Before the files were in those folders but now even when I rescan those folders they apear empty. But when I browse them with a finder or explorer the files are still in their folders. This issue came up on both Mac and ATV2 and even on windows. Is there a bug on the latest XBMC? Is there any solution on this?