Haven't seen that, but look for exploding I/O rates ("iostat 1") to the flash device as a likely cause. My guess would be something trying to write to the flash. If you do see higher I/O rates to the flash, it'd be interesting to see if we can figure out what is causing it, because "That's Bad[tm]".
Yep this is the exact same behavior that I was experiencing. I would type a simple command like ls -l and hit enter, terminal would hang for 5-10 seconds then the command goes through. Same with some simple stuff like mv and cp and even just cd .. would take several seconds to execute.
The marvelous thing about taking an extremely complicated software environment like FreeBSD, and then optimizing it for a particular use case, like FreeNAS, is that it isn't *designed* from the ground up to operate the way you would prefer, so sometimes you run into odd and unexplained things.
There are numerous things it might be trying to write to the disk, including some favorites of mine like massive atime updates, which can be triggered by something as seemingly harmless as a find|grep. We can wonder "why is this" all day long, but it really gets you nowhere. That's kind of why I hinted at something practical you could check to see if there's something obvious that can be isolated. That path leads to fixes.