Of that bunch, autodld (downloading RPMs) and rkhunter (scanning the
filesystem, taking checksums, and looking for changes) are both
passive, certwatch probably shouldn't be updating certificates every
24 hours (but could do, so worth checking!), and logwatch just parses
the existing logfiles - it shouldn't touch the daemons.  That leaves
logrotate as the prime suspect, IMHO, as that definitely HUPs/restarts
daemons after it rotates logfiles.  However, it also tracks when it
was last run and won't cycle a logfile and HUP a daemon if it doesn't
need to - since it's already cycled the logs at 03:54, it won't do so
again when you're trying to run it manually unless you tweak the file
"/var/lib/logrotate.status" first.

Note also that httpd exited within the window for logrotate, which
also seems to point the finger at logrotate, so I'd definitely make
sure that was in tonight's list of disabled scripts, and it might be
worth double checking what update cycle certwatch is using too.

Andy
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