I cannot reproduce this in Ubuntu 9.10, steps:
1. Add three groups test1, test2, test3
2. In Users and Groups select Manage groups and for each group add a user to it
3. Check contents of /etc/group

Is it still a problem for you?

** Changed in: gnome-system-tools (Ubuntu)
   Importance: Undecided => Low

** Changed in: gnome-system-tools (Ubuntu)
       Status: New => Incomplete

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Having trouble adding user to multiple groups at once through gnome groups 
applet
https://bugs.launchpad.net/bugs/196884
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