I'm trying to track down this strange behavoir for years now. Always after installing software-updates the permissions of a lot of system-tools are broken as you can see below. I am reasonable convinced that the machine is not owned by someone else. Regular security updates + grsecurity kernel + pax + daily rkhunter runs. Besides that there is no incentive for an attacker to fiddle in such obvious ways with the system. I installed bastille linux (http://bastille-linux.sourceforge.net/) und tried to deinstall it later, so the problems could be related to that. However I don't see how this can happen in a regular way after updates. System: Ubuntu 10.04, recently updated to Ubuntu 12.04 but the problem persists. Apt-Configuration in /etc/apt/ looks sane to me. But nevertheless - could here be the source of the trouble? DPkg::Pre-Install-Pkgs {"/usr/sbin/dpkg-preconfigure --apt || true";}; DPkg::Post-Invoke { "if [ -x /usr/bin/debsums ]; then /usr/bin/debsums -- generate=nocheck -sp /var/cache/apt/archives; fi"; }; // Makes sure that rkhunter file properties database is updated // after each remove or install only APT_AUTOGEN is enabled DPkg::Post-Invoke { "if [ -x /usr/bin/rkhunter ] && grep -qiE '^APT_AUTOGEN=.? (true|yes)' /etc/default/rkhunter; then /usr/share/rkhunter/scripts/rkhupd.sh; fi" } DPkg::Post-Invoke {"if [ -d /var/lib/update-notifier ]; then touch /var/lib/update- notifier/dpkg-run-stamp; fi; if [ -e /var/lib/update-notifier/updates-available ]; then echo > /var/lib/update-notifier/updates-available; fi "; }; Where do these chmod 000 come from? I'm feeling really uneasy with this problem. root@besen:~# find /usr/bin/ -perm 0 -ls 14721496 196 ---------- 1 root root 192592 Oct 15 11:58 /usr/bin/apt-get 14721144 68 ---------- 1 root root 63848 Sep 13 00:29 /usr/bin/gpasswd root@besen:~# find /usr/sbin/ -perm 0 -ls 1727732 92 ---------- 1 root root 86984 Sep 13 00:29 /usr/sbin/usermod 1727727 64 ---------- 1 root root 57640 Sep 13 00:29 /usr/sbin/userdel 1727719 64 ---------- 1 root root 57680 Sep 13 00:29 /usr/sbin/newusers 1727718 40 ---------- 1 root root 38632 Sep 13 00:29 /usr/sbin/grpunconv 1727728 48 ---------- 1 root root 47088 Sep 13 00:29 /usr/sbin/groupadd 1727724 32 ---------- 1 root root 29584 Sep 13 00:29 /usr/sbin/pwunconv 19031620 84 ---------- 1 root root 81880 Jan 3 2012 /usr/sbin/edquota 14877113 48 ---------- 1 root root 46880 Sep 13 00:29 /usr/sbin/grpck 1727722 40 ---------- 1 root root 38632 Sep 13 00:29 /usr/sbin/pwck 1727730 96 ---------- 1 root root 91464 Sep 13 00:29 /usr/sbin/useradd 19031619 16 ---------- 1 root root 14600 Jan 3 2012 /usr/sbin/quotastats 1727720 44 ---------- 1 root root 42760 Sep 13 00:29 /usr/sbin/groupdel 1727733 36 ---------- 1 root root 34504 Sep 13 00:29 /usr/sbin/pwconv 19031621 80 ---------- 1 root root 77632 Jan 3 2012 /usr/sbin/rpc.rquotad 19030041 76 ---------- 1 root root 73600 Jan 3 2012 /usr/sbin/repquota 1727731 40 ---------- 1 root root 38624 Sep 13 00:29 /usr/sbin/grpconv 1727725 56 ---------- 1 root root 49472 Sep 13 00:29 /usr/sbin/vipw 1727723 64 ---------- 1 root root 57672 Sep 13 00:29 /usr/sbin/groupmod root@besen:~# find /sbin/ -perm 0 -ls 16760927 76 ---------- 1 root root 73464 Jan 3 2012 /sbin/quotaon Any tipps? I really can't pinpoint the problem in more detail. It happens after installing updates but I can't find no hooks in the dpkg/apt system.