It worked itself out..
The system problem eventually was that,
1x64gb SSD boot drive
1x640gig Apps drive.
I however moved some files like user apps and what not following a SSD guide to clean up space on the drive.
This inadverntly maked the drive (640g) as a system drive.
Having not realised that,
I installed my RAID-0 (2x64SSD),
It seems even tho the original 64gb was formatted into the raid, and a new o/s installed onto it.
When windows gathered it's information it included the 640g drive as being needed, since it was marked as system.
Long story short when I made the disk inactive it killed the raid,
when I re-installed the raid and made the drive active again, it was still a system drive.
Turning it off again, killed the raid.
That's when it struck me, so I used a boot cd to clear the partition/volume and everything about the damn drive (640g).
Re-installed everything, and things are fine now.
Well fine as in, I'm up and running and yet to start a backup... until all the updates are installed.
I'm sure the problem will be gone tho.