i cant beleive one file well be handled any different from another file, so ill say again you should invest some time in checking what or where in these files it becomes errored.

Just saying it came out bad, doesnt a make it so, this as easy as pie could be your system causing it, I once found a problem I thought was in network traffic from one machine to another, turned out it was in a scsi driver software, while i was writting the data to the disk.