Cron doesn't have permissions to execute workflow state changes

This is not a scheduler issue per se, but I'm sure people have experienced this before. Cron runs as anonymous and therefore isn't allowed to do most workflow changes...well, none in fact.

I'm a bit baffled why this is only an issue for us with scheduler-workflow and not with lots of custom code we do also run on cron and an anon user wouldn't have permissions to execute - it just works.

Can anybody shine any light on this? I could easily load a user with the right permissions on scheduler cron, but I'd like to understand the issue first...

Thanks!