It seems that there were two issues in my case:
1. FreeNas main interface did not use ipv6 autoconfigure.
2. My ancient macbook had ipv6 turned off all together, which was a bit surprising, I didn't even consider this.
After fixing these settings everything works like a dream. AFP is rock solid and time machine hasn't failed since. Also i enabled some of my jails and it doesnt seem to interfere. However the jails still produce an error message when started. Need to do some more digging.