I have used the setup wizards and modified the keys for "setjambamaster" "jambastrobe bla bla." But I find that I constantly have to hit these buttons to make my toons follow my current char. When I swich window the new toon (2) becomes master. Which is fine I guess, but when I swich back to the "main" all toons still think the other toon (2) is master. So I have to manually set my main to master again.
I believe this has to do with the speed of switching. If I switch through a lot of different windows very quickly, I notice that the Jamba Master doesn't instantly change every time. That's not so much of an issue as if you're using strobing though. Both of these are hampered (slowed down, impeded) by using the Jamba "all" tag to tell the other characters to set the master and the same for follow strobing.

Any tips how you guys control your group with ISboxer and Jamba?

My solution to the fear problem was to disable follow strobing, putting the group out on one side, and controlling my "main" when it got feared.

Im considering turning of the followstroping, and making a seperate follow button as I used to have to control when my toons should follow the char im currently controlling.
You know, even after automatic transmission was invented, many people still buy cars with manual transmission. That's because the automatic version sucks in various situations, where manual will give the driver full control over what's happening.

I don't use strobing because I prefer the level of control that an auto-follow key gives me. It's one of my 3 most important keys, which are Follow, Assist, and DPS Spam. If you watched me during combat, my left hand is almost exclusively pressing those 3 keys, with one finger on each. Also, many times I like to switch characters around and do different things on each, and having the others auto-follow me when I switch would be annoying. For example, doing collection quests if I'm right by like 3 objects on the ground that each guy is supposed to be collecting, I try to minimize my total time by running up to 1 and looting with one guy, and while he's busy with that I can loot with another guy. If the first guy turned around and followed, that would defeat the purpose

With that i mind, I will say that I am keeping all of these issues in mind and will make better solutions available as soon as I can

also, can you put a popup text in the Repeater profile to make it popup when you toggle repeater on or off?
Instead of adding additional features to the built-in repeater hotkeys, the functionality available to Mapped Keys is extended. The Quick Setup Wizard for example gives you Shift+Alt+R to toggle Repeater, and it has a popup text action.