It sounds like the SS4200-E has failed in some way. Without the HDDs connected you have just the SS4200-E booting from the Disk on Module (DOM). That's about as basic as you can get. The SS4200-E has a three year warranty, you can contact Intel Customer Support and request a replacement if your's is within three years old.
If you do get a warranty replacement, just put your existing HDDs in the same locations and you should be good to go.