There is no doubt that a skill challenge is an encounter and would normally count towards a milestone. However, if the skill challenge is trivial, then like a trivial combat encounter the DM is under no obligation to count it as progress towards a milestone. If the complexity of the skill challenge is lowered enough to make it two to three levels below the level of the party, then the skill challenge is too easy, and like a too easy combat encounter also, IMO, fails to qualify towards a milestone.