The usercounter in the groupfiles is changed when "site adduser/deluser/chgrp" is called. Any scripts that change groups for users, or adduser/deluser, have to edit the groupfiles themselves.
For example, my ioGui.iTCL script that allows u to copy an existing user, doesn't update the usercounter in the groupfile, so if u copy 100 users and then delete them, the counter will be at -100 or so.
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