When going to swap HBAs I noticed mis-matched cables. So what I had done is connect one HBA to both front and rear backplanes, then connected the front backplane again to a second HBA. So the timeout was the second HBA wanting to connect the disks, but the disks were already on the first HBA.
Silly mistake, I removed the unnecessary HBA and cable, and it works great now
Cheers, thank you very much for your help. You pointed me in the exact right direction!