I publish my calendars on Safari and everything is good, but when I add the server info ect. to iCal only one of my published calendar shows up. In the past all of the calendars showed up until I added privilege sets to prevent this. This is also unusual, because it is not always the same calendar - it changes on startup.

Well privilege sets can be used to show which calendars shows up...

http://www.seedcode.com/pmwiki/pmwiki.p ... Privileges

..restricting them as necessary. But a different calendar each time? That's kind of interesting. What is the calc you're using in the privilege set to restrict access?

Sorry... I was unclear. This time I do not have any privilege sets which baffles me as to why this would happen.

I'd delete your CalDAV accounts in iCal and re-plublish. That should clear things up, restarting your FMS if that fails.