I'm still setting up my device and am having the same issue. Most transfers to the device have been via Robocopy and are all successful, but browsing the shares through the Windows explorer interface later I've found that a couple folders have disappeared (like the Video folder under Media). If I browse through the dashboard I can see that the folders and files within are present. Additionally, if I browse the network and manually enter the path through the "missing" folders I'm able to access them. I've confirmed that the folders are not set as hidden or system files in Windows. I've also checked the box(es) to show hidden files and folders in both Windows and the Dashboard just in case. The device has been cycled a couple times, but that didn't work. Finally, I've not even implemented share security yet (or created user accounts) so the device is literally wide open to all users. The behavior does not make sense.
I'm very interested to know what your case reveals and whether there's a bug, conflict or fix found.
Device: ReadyNAS duo v2
Software: RAIDiator 5.3.3
RAID Type: X-RAID2
Host OS(s): Windows 7 64-bit