One wonders whether all the file corruption you mention was done on one occasion or several. I cannot help wondering if, at some point, you thought everything was done and turned off the affected hard drive in question while ignoring Windows telling you that it was still in use, or else forced a shutdown when Windows was taking forever waiting for "background programs" to close. Windows loves to tell you that the hard drive is in use even though you find no applications via task mgr using it. Do you always dismount the drives using the Windows gui? Have you ever accidentally powered off one of them, or even intentionally done so because you "thought" nothing was going on?
If your memory is okay, my SOP would be, first, to run a complete check disc on your pc: check the box that says "scan for and attempt recovery of bad sectors." That will take a while. Next, do so with the external drives, first with the one that had the bad files. That may take a day or longer if you are using usb 2, but don't skip it.
While check disc is scanning the one drive, do a complete anti-malware scan--including a scan of the other external drive, the one check disc is not checking--with your resident program, followed by a complete scan with Malwarebytes and Superantispyware. When check disc is through with the one drive, do the complete multi-scan for malware on it. Once everything is done, I would also defrag all the drives: if you have pieces of one file in 800 different places, that makes it difficult for Windows to keep up, and, with large files, it is much more likely that the files in question will be fragmented. Keep the external drives defragged.
You did not mention whether you can replicate the errors. Do errors only occur when copying to a certain hard drive?
I forgot to mention one other thing about what I consider to be SOP: run sfc after you run check disc, and then run KB947821. I run both of those religiously, but you do have to check every now and then to make sure there's not a new version of KB947821; the most recent version was published on 08/23/11.