In FreeNAS 9.3, the recommended boot disk in 8G and no longer 4G.  If you have an existing FreeNAS installation that only has a 4G boot partition, you will have to increase it for FreeNAS 9.3 to work properly.  I have my FreeNAS running as a VM.

Edit the settings in vSphere for the VM

1. Increase the vm disk to 8G
2. Reboot VM

Check Partition

root@csu-s:~# gpart show -p da0
=> 34 16777149 da0 GPT (CORRUPTED)
   34 1024 da0p1 bios-boot (512k)
   1058 6 - free - (3.0k)
   1064 16776119 da0p2 freebsd-zfs (8G)
You should see the "CORRUPTED" label

Fix Partition

root@csu-s:~# gpart recover da0

Grow Partition

root@csu-s:~# gpart resize -i 2 da0
gpart: Device busy

If you see "Device busy", the do:
root@csu-s:~# sysctl kern.geom.debugflags=16
kern.geom.debugflags: 0 -> 16

root@csu-s:~# gpart resize -i 2 da0
gpart resized

Reboot VM

root@csu-s:~# reboot

root@csu-s:~# zpool scrub freenas-boot

root@csu-s:~# zpool set autoexpand=on freenas-boot

root@csu-s:~# zpool online -e freenas-boot da0p2