There has been much debate on this cloudiness issue. Even a representative from Five Star Chemicals has said that as long as the solution stays AT OR BELOW 3.0 pH it's good to go. Cloudy or not.
Minus it looking weird, and maybe being hard to find small things in a big batch of it, I don't see what the fuss is about star san being cloudy. When I make up a 5 gal batch by the next day it's cloudy, and then I proceed to use it for 3 or so months and never had any issue. Even then I only get rid of it because I think 3 months per batch is good enough, but even then the pH is still at 3.0.
Don't fear the foam
Don't fear the cloudy