I mentioned one way to reproduce the issue of a pool not properly mounting if you didn't export it earlier (
http://forums.freenas.org/threads/ecc-vs-non-ecc-ram-and-zfs.15449/page-4#post-85375)
Here is another, this time only using FreeNAS.
Create a zfs pool (RAIDZ2 , 6 drives), using 6 ports on a LSI adapter (X10SL7-F supermicro motherboard). Create the pool using the device name (and not the gptid, which is typical on how a pool would have been created in another system)
zpool create pool raidz2 da0 da1 da2 da3 da4 da5
halt system.
plug it into another machine (identical to machine #1, also running freenas (9.1.1)), this time however, connect 2 disks to LSI adapter (da6 and da7) , and 4 disks to intel adapter (ada0 ada1 ada2 ada3).
boot. pool won't mount as it wasn't exported earlier, so you have to use zpool import -f poolid pool (I already had a zpool named pool on the 2nd system, so couldn't do zpool import pool)
now halt second system.
Put back the 6 drives in the first machine.
However, put it such as the first 3 drives are back on their original LSI sata ports (da0 da1 da2); and the 3 remaining disk are put on the 3 intel SATA ports (ada0, ada1, ada2). Boot
pool has been imported but is degraded; doing zpool export pool followed by zpool import -f pool and all is good and back to normal.
Similar scenario as what I had done with linux earlier in the end...
It's unlikely someone who has only ever used freenas GUI would experience such scenario, but you never really know how or where the pool got created in the first place. It's also not uncommon for people to create their pool using the command line, such as when using a partition rather than the full disk (GUI doesn't let you do that)
So really... Export your pool if you can before using it in another system or changing hardware. Probably won't do anything if you didn't, but will save you heaps of headaches if you do in the event you do have issues.
That's what the manual state anyway, and as everyone knows, you should always follow the manual to the letter :)