I have some cron jobs which are just not run according to the AOE_Scheduler module. What can be the reason? Some others are running so it does not seem to be a general problem.
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So this question would have an answer....
The problem is most probably caused by a cron that takes too long.
And other cronjobs that should run after the "long one" do not get scheduled because it's too late to schedule them.
The error message comes from
Mage_Cron_Model_Observer::dispatch(), when this evaluates to
$time < $now - $scheduleLifetime ($time is the time set for the cron and
$scheduleLifetime is the value you set in the backend for
Missed if Not Run Within in the cron configuration). Try increasing the lifetime or move your cron to an other hour.
An other solution would be to wrap all your crons that should run close together in one single cron, and give it time to finish.