Missing 'Place auto-renewal tasks' on domains

[iso99]

This happens regularly especially if I'm tweaking around .htaccess and other server config settings.

When it fails to run cron, the 'Place auto-renewal' tasks are not added to the domains set to expire in X days.
Running cron manually doesn't  work either.

Any suggestions?

[BRJP]

What are you tweaking in the .htaccess files and system configuration?