How is your technique when running with the minimal trainers? Is it possible you are staying up on your toes pretty much the whole time? You need to ensure the heel makes contact with the floor, (obviously after the forefoot) but if you are up on your toes the whole time you run that would be very hard on the calves.
Also what foorwear do you use for normal day to day wear? I switched to flat shoes pretty much 100% as I found it helped to keep my calves stretched. If you wear shoes with heels all day you wil be shortening the calves, then asking quite a lot of them to run with a much flatter shoe.