If you can, get the md5sums.txt files for the corrupt clips. They should have been made at the time the footage was downloaded from the cards with R3D Data Manager. From there, you'll be able to verify the files you have to see if they have been corrupted at some point. Even if the transfer from the CF cards worked perfectly, the transfer from there to a second hard drive could have corrupted the files. It has happened on shoots I've been on.