To keep the R3's racy handling, Cérvelo's engineers managed to maintain the same short chainstay length of 405mm, rather than having to shift to the longer 415mm recommended by disc brake manufacturers. Cervélo achieved this by using a custom FSA SL-K crank with a 5mm offset to ensure the correct chainline.
http://www.bikeradar.com/road/news/arti ... -r3-45087/
the CAAD12 chainstays are 40.5 - they don't seem to think this chainline modification is necessary.
Haven't heard any reports of problems.