You can write an alternation script (or ask someone to do it) or use round-robin as Group Start option to alternate between the groups. The latter is the easiest. Say you have two groups. Then you add a group start option for the first group: cycle-round-robin, position 1. And for the second group: cycle-round-robin, position 2. That's it. (To find the place where you can add these start options press the 'Group Start Options' button in the Group Editor.)
Thanks for your help Kotori. I have founding the script machine effect on the native site, but wasn't able to use it.
With your explanation (I must say that I'm not a kontakt "editor" at all!), I located it in my program.