I have an Iomega "Home Network" NAS drive, firmware version K1.08 L1.0 W1.5 attached to my network via a wire, as is my boxee'd Apple TV. I have it set up in Boxee as an SMB attached media source. The apple TV is at version 2.6 and Boxee is the latest "test" release 0.9.9.5324, although the problem also occurred in the previous release I had.
The problem is that I can only see some of the folders and files on the drive. For instance, I have the content divided into 4 folders, but only 3 of them are displayed. Within the folders I can only see about 3/4 of the files they contain. I can get Boxee to display different folders/files by renaming the missing files, this will sometimes make the missing file appear and some previously displayed files disappear. I can't find a naming pattern that will consistently work, but the file names definitely affect the problem. None of the names are especially long or anything, they are just the name of the movie or video. It also happens to all file types, including iso, etc.
I copied the whole file structure to my Windows XP SP3 PC and added that as a SMB media source and all of the files display normally in that case.
I also went into XBMC and set up the NAS as a source and I can see all of the files there, so it is something between Boxee and the Iomega NAS.
I am not sure what technology the NAS drive enclosure uses, I think it might be linux because to work the actual hard drive has to be formatted as a FAT32 drive, it won't work if the drive is NTFS. There are several older versions of its firmware available, I tried updating the drive with them but the problem occured in all versions.
Weird! Let me know if you want logs or anything (and how to dump them).