I don't know much about the TS1400D model. I've not used it. I assume the shared folder permissions you're talking about are in the buffalo web console, and not in windows itself.
Try logging out of the device, clear your web caches, and login again.
I've not used any TS joined to AD before. For that one, maybe you need to remove it from the AD domain and rejoin it to the domain.
If all else fails and the problem didn't happen with 1.65 or older firmware, maybe you could revert one of the units back to an older firmware.
If the folder permissions you are talking about are in windows on the security tab, then that's an MS/AD account issue.