I just tried out Defraggler and seem to have a serious problem now. I ran defrag on an external 1 tb HDD with NTFS and watched it for a while. After a few hours I came back and noticed a "Data has been lost, writing H:\$mft failed" (translated into English, not exactly like that).
Now I can't access my data. I did not reboot my Laptop afterwards... are my files finally gone?
Seems like your suggestions helped... after a reboot I could check the disk and chkdsk repaired some failures. After that and another reboot I could access them again and hope, all are well. I think, the problem did occur from an USB-Hub. It probably was not prepared to transfer lots of files for hours...