Every couple seconds it sounds like something writes to all the drives. When that happens the blue lights turn red, then quickly back to blue. This cycle is endless.
It is. The default ZFS tunables in FreeNAS cause it to close out transaction groups at a maximum lifetime of 5 seconds, so you'll see writes about that often, even if it's just a brief bit of metadata.
The .system dataset starts on the boot volume, but gets relocated to the first pool created after install. You can check under the web UI from System - System Dataset or from SSH via zfs list.
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