The 16GB has been in my 40D and is and always has been reading fine from my CF card reader. I have 3 cards, a Sandisk Extreme III 16GB, 8 GB and a 4GB. Although it was my backup camera (for that card anyway), my other two CF cards worked fine, one even from the same camera body.
I just had a near heart attack when a CF card from yesterday's shoot didn't want to read in my PC.