I don't think the lens would matter for video. It just needs to be able to write at a certain speed (which isn't that fast to begin with). I'm using an older 16gb transcend "133x" card and it works fine with 1080p. I just can't record video AND take an 18mp snapshot (raw+jpg) at the same time, else the video clunks out cuz of write speed problems.
But the way you describe the video being corrupted, it's quite possible something might be amiss with your CF card. And if after ruling out it's not the CF, then at least you know you've done as much as you can to test out the puppy before sending it into Canon for eval/fix.