If you're launching D3 using Battle.net (I can only assume you're aware from the
D3 Quick Start that you can bypass the battle.net launcher?), then...
a) ISBoxer must launch battle.net (CLOSE IT FIRST IF IT IS RUNNING)
and b) battle.net MUST EXIT after each game instance.
Here are Step by Step instructions...
1. Exit Battle.net if it is running
2. Launch your ISBoxer Character Set
3. The first Battle.net instance should come up. Log in, click Play on Diablo 3.
4. The first game instance should come up
5. The first battle.net instance may not have closed -- for future launches, you can enable the "Exit after launching" option in the battle.net settings (you must do this for each Character, because ISBoxer is keeping separate battle.net settings for each, and it will also not affect your non-multiboxing settings).
6a. If battle.net automatically closed, this process should repeat from #3 until your team is fully launched.
6b. If battle.net did NOT automatically close, you must repeat the process from #1 for ISBoxer to continue launching the games -- leave the first game instance open, exit battle.net, launch your ISBoxer Character Set
Do note that the first time you launch a team, ISBoxer may need to copy the Cache folder, which could take a couple of minutes.