Interesting..Ok. The short answer is that you can't have a bunch of eggmobiles in one room and expect for them to work properly. However, what I think you can do is use the "no more enemies" linedef to create new rooms for a bunch of bosses.
What on Edge was saying about the multiplayer flag is the one in the SRB2DB that says "end level on death". If you check that, and have one boss, it will literally do just that.
Oh, and when I said don't check flags that aren't described, don't check the "deaf", "Thing flag", or "multiplayer" flags unless you know what you're doing. Usually, they will screw up what an object is suppossed to do. For example, if you check the deaf flag on a jetty-syn gunner, then it won't move.