Raid1 booting problems

Hi guys
Im close to giving it all up unless someone can help me!
I have got 2 80GB HDDs connected via SATA to a PCI Raid card. I have ran the setup and had it working but now it only boots every few tries! I cant seem to sort a pattern! If I put the cables directly into the motherboard it boots fine and shows 2 disks which are identical in their file structure and data. Then If I shutdown, reconnect the cables to the card and boot it boots without fail.

Its the first time i have had to do this from scratch as all the other machines I have had this with have been prebuilt servers and im just totally lost as to what to do next!