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I've had three instances of CF card failure or corruption. In each case I rounded up the usual suspects - the card itself, the camera, the card reader, the USB cable, the xfer software, etc., and swaped out componets one at a time trying to find the culprit.
In every case, the problem ended up being the pin connections. Never the solid state memory on the card, never the USB cable, never the software.
One case was failure of the card connector (male pins) inside a Canon 5D2. Problem started intermintent, then became permanent. The 5D2 would refuse to recognize 2 of 6 CF cards I fed it. Yet other cards would work in the 5D2 and the cards the 5D2 rejected would work in other cameras.
Cost me $100 to have the 5D2 pin connector replaced by unitedcamera.com. During the transaction I had a good conversation with their repair tech. He said that 90% of CF card failures are due to connecton problems. Either bent or corroded male pins in the camera or card reader, or fouled female slots in the card itself.
Corrosion or dirty slots can often cure themselves. You stick that CF card in pocket, a dust bunny gets in there, you insert it into a camera or card reader and one or more pins are dead. You remove and re-insert a few times, and volia, the problem goes away. Ditto with corroded mail pins. After a few re-insertions, maybe the corrosion is cleared.
Why a single pin failure is not automatically detected by hardware or software is a mystery to me. I don't know what happened to parity bits or checksums from the old days, but examples are everywhere showing corrupted image data or scrambled file directories that are the result of a single bit failure somewhere in the xfer path.
Yours sounds strange in that part of the card contents were OK and part was not. But may people have reported random corruption of just a few images out of hundreds on a card. A possible, but less likely cause may be a static hit on the card. When you handle a card, it's possible that a small static charge can transfer from your hand thru the card, wiping out random bits.
So don't pet your cat on a dry, cold day and then grab your camera.