Disk not ejected properly error and then the OS hangs during certain tasks

Got a Mac Pro 5,1 Areca 1880ix-12. Four internal 3.5" running in RAID5 and two SSD's, one is running off the Areca in pass through mode and the other connected to the motherboard backplane.

I have unplugged the RAID5 array, leaving only the two SSD's connected but the error still persists. It's random, sometimes does not happen at all, at other times pretty soon.

Error looks like so:



What could be causing this? It hangs certain parts of the OS, like won't shut down and the beach ball of death appears. I have tried ejected the SSD with Windows on it and any other NTFS volumes, does not help. Have also performed a clean OSX re-install.