Actually I had this problem too. I have never suffered bad skin and before this woe did eat a lot of chocolate and pasta/rice/spuds etc. At Uni I ate loads of crap - you name it pizza, hotchips by the kilo, and my skin never broke out...then I started atkins and all of a sudden I was getting one spot at a time every other day or so...it freaked me out!

However it has all calmed down now and i cut down on cheese and processed meats and increased the WATER and variety of veggies. I also cut down (quite coincidentally) my working hours and relaxed more and now my skin looks better than pre-ATkins. So you are not alone, but I dont think it is something that will become a real problem!