Under Gentoo adding a user work fine, but when removing it using the gui,
most of the groups where removed.

For the following example I worked with a new user called mikene.  Was the
only one desired to be modified on the user files.  I created it with
defaults settings (no additional subgroup selected) at creation, or removal.

1) Add the mikene user using default settings, the changes are below.

File changes after adding the user:

# diff -u /download/etc/passwd passwd
--- /download/etc/passwd        2003-12-16 15:47:41.000000000 -0400
+++ passwd      2003-12-16 16:14:04.000000000 -0400
@@ -43,3 +43,4 @@
 p2p:x:1002:100::/home/p2p:/bin/bash
 sshd:x:22:22:sshd:/var/empty:/dev/null
 cvs:x:1003:408:added by portage for cvs:/home/cvsroot:/bin/false
+mikene:x:1004:100::/home/mikene:/bin/bash

# diff -u /download/etc/group group

This indeed show the user was created right.  

2) Open again the gui, and remove the user mikene, apply settings.

File changes after removing the user:

# diff -u /download/etc/group group
--- /download/etc/group 2003-12-16 15:47:40.000000000 -0400
+++ group       2003-12-16 16:16:10.000000000 -0400
@@ -1,51 +1,14 @@
 root:x:0:root
 bin:x:1:root,bin,daemon
 daemon:x:2:root,bin,daemon
-sys:x:3:root,bin,adm
 adm:x:4:root,adm,daemon
-tty:x:5:mariov
-disk:x:6:root,adm
 lp:x:7:lp
-mem:x:8:
-kmem:x:9:
-wheel:x:10:root,mariov
-floppy:x:11:root,mariov
 mail:x:12:mail
 news:x:13:news
 uucp:x:14:uucp,mariov
 man:x:15:man
 cron:x:16:cron
-console:x:17:
-audio:x:18:mariov
-cdrom:x:19:mariov
-dialout:x:20:root,mariov
 ftp:x:21:
-sshd:x:22:
 at:x:25:at
-tape:x:26:root
-video:x:27:root,mariov
 squid:x:31:squid
-gdm:x:32:gdm
-xfs:x:33:xfs
-games:x:35:
-named:x:40:named
-mysql:x:60:
-postgres:x:70:
-cdrw:x:80:mariov
-apache:x:81:
-nut:x:84:
-usb:x:85:mariov
-vpopmail:x:89:
-users:x:100:games,mariov
-nofiles:x:200:
-qmail:x:201:
-postfix:x:207:
-postdrop:x:208:
-smmsp:x:209:smmsp
-slocate:x:245:
-portage:x:250:portage,mariov
-utmp:x:406:
-proftpd:x:407:
-nogroup:x:65533:
-nobody:x:65534:
-cvs:x:408:
+users:x:100:mariov

# diff -u /download/etc/passwd passwd
--- /download/etc/passwd        2003-12-16 15:47:41.000000000 -0400
+++ passwd      2003-12-16 16:16:11.000000000 -0400
@@ -15,31 +15,5 @@
 cron:x:16:16:cron:/var/spool/cron:/bin/false
 ftp:x:21:21::/home/ftp:/bin/false
 at:x:25:25:at:/var/spool/cron/atjobs:/bin/false
-squid:x:31:31:Squid:/var/cache/squid:/bin/false
-gdm:x:32:32:GDM:/var/lib/gdm:/bin/false
-xfs:x:33:33:X Font Server:/etc/X11/fs:/bin/false
-games:x:35:35:games:/usr/games:/bin/false
-named:x:40:40:bind:/var/bind:/bin/false
-mysql:x:60:60:mysql:/var/lib/mysql:/bin/false
-postgres:x:70:70::/var/lib/postgresql:/bin/bash
-apache:x:81:81:apache:/home/httpd:/bin/false
-nut:x:84:84:nut:/var/state/nut:/bin/false
-cyrus:x:85:12::/usr/cyrus:/bin/false
-vpopmail:x:89:89::/var/vpopmail:/bin/false
-alias:x:200:200::/var/qmail/alias:/bin/false
-qmaild:x:201:200::/var/qmail:/bin/false
-qmaill:x:202:200::/var/qmail:/bin/false
-qmailp:x:203:200::/var/qmail:/bin/false
-qmailq:x:204:201::/var/qmail:/bin/false
-qmailr:x:205:201::/var/qmail:/bin/false
-qmails:x:206:201::/var/qmail:/bin/false
-postfix:x:207:207:postfix:/var/spool/postfix:/bin/false
-smmsp:x:209:209:smmsp:/var/spool/mqueue:/bin/false
-portage:x:250:250:portage:/var/tmp/portage:/bin/false
-guest:x:405:100:guest:/dev/null:/dev/null
+squid:x:31:31:Squid::
 mariov:x:1000:100::/home/mariov:/bin/bash
-nobody:x:65534:65534:nobody:/:/bin/false
-proftpd:x:1001:407::/home/ftp:/bin/false
-p2p:x:1002:100::/home/p2p:/bin/bash
-sshd:x:22:22:sshd:/var/empty:/dev/null
-cvs:x:1003:408:added by portage for cvs:/home/cvsroot:/bin/false


Many of the groups where removed, even many of them that do not have any
relation with the user created.  Also the problem is so severe that even
root info is lost and there is no way to log/su as root after the changes.

Even work directly with the xml file as suggested on bug # 122389, but
changes I do to the file by hand are applied without problems.  .  I will
work more closely with the backend xml and see if found the problem.

My system is Gentoo 1.4 compiled from scratch with that version, and
running unstable packages updated twice a week.