I Have looked at the raid log and nothing seems to have gone wrong. It is a single Areca with 16 sata drives - the web log doesn't show any errors and two Raid6 volumes are healthy.
We feel it is just something stuck in the system volume. Don't know what to do next to get rid of this no system volume problem.
Upgraded to latest version of iscsi-r3 as per instructions from support tonight. All looks same, no improvement.