If soreness was an indicator of intermediate status, all CrossFitters would be intermediate. Soreness is the result of eccentric loading, and persistent soreness is a the result of the lack of recovery, most often related to an inadequate protein intake. Count your protein intake, and make sure you're getting at least 1 gram per pound of bodyweight. What might have been adequate previously may well be inadequate as you approach the limits of 48-hour recovery.