I know this is probably unrelated to the problem you're having, but how are you connecting the drive? Do you use USB or does the device have an eSATA port? Personally I dismantled one of those devices, and took out the HDD because the USB transfer speed was simply too slow (I was getting like 24MB/s with USB2). I later connected the disk directly to the PC over a sata cable.
Back on topic. I suspect the problem if somehow related with your file system. Personally I haven't had any problems with NTFS on linux yet, but its also true I don't use that fs very much. Before you go any further I strongly suggest you try to create an image backup of your drive.
dd if=/dev/sdX of=/mnt/external_disk/backup.img
Make sure you have enough space on the target device. In case something happens with your file system you'll have something to revert to. Also it would be interesting to see how fast an image backup can be made.