I have been faced with similar uptime issues on my machine, but solved it more 
cleanly.

Once Anacron is doing its thing cron leaves it alone. Once anacron is done cron 
resumes normal operation.
It uses the pgrep utility from the required procps package for that so no extra 
dependancy.

--- crontab.dpkg-dist   2006-12-20 01:02:42.000000000 +0100
+++ crontab     2008-02-15 08:34:43.000000000 +0100
@@ -9,9 +9,9 @@

 # 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 )
+25 6   * * *   root    pgrep anacron || ( cd / && run-parts --report 
/etc/cron.daily )
+47 6   * * 7   root    pgrep anacron || ( cd / && run-parts --report 
/etc/cron.weekly )
+52 6   1 * *   root    pgrep anacron || ( cd / && run-parts --report 
/etc/cron.monthly )
 #


Regards,
Jaap



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