Transfer speed from CF to computer is a function of your card reader, and the files sizes of your images. Setting the sharpening, Pictures styles, ALO, etc type of settings do NOTHING to the raw files, except for turning on a little flag embedded in the RAW file that says the setting was used. Your files sizes should not increase by doing this.
In this case, I think that this is a perceptual slowdown, rather than a real one. BTW, I can fill up a 2GB card, and it still only takes about a minute of less to transfer 2gb from my reader to PC (and these are with Sandisk Ultra II's which are their slowest models). I'm not sure how much data you have on your cards for it to take 20 minutes. Also, are you transferring at USB 1.1 or USB 2.0 speeds?