If you want to have a unique boss (i.e., a boss with a name that is different from just your normal bosses), you can't have him in the same group as the rest of the "mission mobs." You have to put him in a separate group all his own. Otherwise, you'll get him spawning multiple copies like you saw.
As to why he scaled down to a lieutenant, that's how the MA works. Bosses scale down to lt's, even on large teams, if the team leader is on the first difficulty level.
Thanks. I kinda of thought about that. Just hope the group name can be the same. I'll give it a try.
Group name can't be the exact same since the group name is also the file name. What I did was took the group name and added Elite to the end for the unique bosses for mine.
I actually did the exact same thing 
Thanks for the reply
During solo testing this did not happen. When I published and had a team of 4, my custom boss was scaled down to a Lt. and was spawing with all of the patrols. I went back and checked the settings but it all looked right. Any idea why this might be happening and how to fix it? I don't want to publish a broken arc.