Just to add some info since original is a very plain. So according my
theory something halts the scripts and the weekly and daily crons match
which explains at least why I`m getting this only on weekly basis.
Output

r...@wolfdale:~# uname -a
Linux wolfdale 2.6.32-24-server #42-Ubuntu SMP Fri Aug 20 15:38:55 UTC 2010 
x86_64 GNU/Linux
r...@wolfdale:~# date
Sun Sep 12 22:22:48 EEST 2010
r...@wolfdale:~# cat /etc/crontab 
# /etc/crontab: system-wide crontab
# Unlike any other crontab you don't have to run the `crontab'
# command to install the new version when you edit this file
# and files in /etc/cron.d. These files also have username fields,
# that none of the other crontabs do.

SHELL=/bin/sh
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin

# m h dom mon dow user  command
17 *    * * *   root    cd / && run-parts --report /etc/cron.hourly
25 6    * * *   root    test -x /usr/sbin/anacron || ( cd / && run-parts 
--report /etc/cron.daily )
47 6    * * 7   root    test -x /usr/sbin/anacron || ( cd / && run-parts 
--report /etc/cron.weekly )
52 6    1 * *   root    test -x /usr/sbin/anacron || ( cd / && run-parts 
--report /etc/cron.monthly )
#

r...@wolfdale:~# test -x /usr/sbin/anacron || ( cd / && time run-parts
--report /etc/cron.daily )

##### MEANWHILE ######
root     19549 14357  0 22:25 pts/0    00:00:00 bash
root     19550 19549  0 22:25 pts/0    00:00:00 run-parts --report 
/etc/cron.daily
root     21795 19550  0 22:27 pts/0    00:00:00 /bin/sh /etc/cron.daily/apt
root     21816 21795  0 22:27 pts/0    00:00:00 sleep 1458

/etc/cron.daily/apt dosen`t contain any sleep 1458 command so it is coming from 
somewhere else, unfortunately I`m unable
to track it since I`m not very aware of this freak of nature called anacron. 
Could someone explain if it has debug mode or something? Suggested workaround 
is to move weekly cron with 1h. to say -

47 7    * * 7   root    test -x /usr/sbin/anacron || ( cd / && run-parts
--report /etc/cron.weekly )

and monthly with another

52 8    1 * *   root    test -x /usr/sbin/anacron || ( cd / && run-parts
--report /etc/cron.monthly )

This isn`t tested yet, but simple math shows that if daily cron halts for 24,3 
minutes the weekly cron which is 22 min after daily
will collide with daily. I`ll try that tonight or tomorrow.

-- 
start: Job is already running: anacron
https://bugs.launchpad.net/bugs/606491
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