. . . but simply copy from the card to the desktop about half the files get corrupted...
Copy files from card to computer/drive using only the finder (i.e., drag & drop). If the images are from a Canon camera, and you want to select only certain images, use Canon's EOS Utility.
Capture One isn't the best tool to browse files on a memory card. Its normal process is to create sub-folders and generate thumbnails and previews of every image, which is very inefficient for simply copying images from a card.
If you are paranoid (like I am) then do a test. I recently bought new 16GB CF cards and one of them corrupted files while shooting. I thought it was the camera and after extensive testing of all the cards, and tethered testing, realized it was the card itself.