Yeah that navigation deal is sort of a known issue. I thought there was already a ticket for that, though it was for the Cron package (Cron, Backup, and Shellcmd were all written by the same guy). If you open a ticket make sure it's under the "packages" area (http://redmine.pfsense.org/projects/pfsense-packages) since that is am issue with the individual packages' code and not an issue in the base system.
I'll have a look at the boot log more in depth later, but a quick scan of it looked OK.