Also after Sorkin left Tim was producing With Out a Trace and John Wells said it could be hard to schedule around. They had to do a lot of work to fit him into the schedule for the final season the Danny and CJ's storyline could be finished up.

He came in and out a lot. He was in the first season and the last season and then sprinkled in between.
Don't know if there was ever an official reason. But what they said about Sorkin was that since he wrote every teleplay (of the seasons he was present for) himself, and he usually turned them in late, often guest stars that he wanted to use were unavailable and their characters were not able to appear in some episodes. Don't konw if Danny Concannon's absense can be explained by that, but it's why other people came in and out a lot.
He was so great on The West Wing.

He didn't. His character just wasn't written into the story by Sorkin at times.