What RAID controller are you using? The RAID mode built in to your intel motherboard is probably "software RAID", which means the OS has to boot and load the RAID drivers before the RAID setup will work. This is not an issue with RAID 1 setups, but it means that you cannot have a RAID 0 boot drive.
Also, I believe RAID mode on your Intel chipset automatically enables AHCI. If you were using your single C300 in IDE mode, then your restored backup of Windows will try to boot without the necessary AHCI drivers and will fail. You can fix this by booting from a Windows 7 install disk and selecting "Repair Windows".
Using the intel controller, and thanks for the reply I did fix the problem just reloaded windows completely and then tried to restore from my backup which only partially worked for example some desktop apps didnt come back from the restore at all, some came back but dont run, and some work fine. But I have most of my stuff backed up elsewhere that was manually saved instead of autobacked-up by windows so just reinstalled the programs from those sources. Kind of strange but im 90% back to my old desktop, But thanks