reinstall Windows but on restart no boot found

The small drive is probably a SSD to increase the system performance.
It can be used to host part of the OS or as a cache drive.
As it is a laptop, don't you have the factory recover disks?
Please give us the brand and model of your laptop.

Yes thats correct. There are 2 physical SSDs, the other drive is the USB Windows & Installation. The problem is the small SSD is somehow the primary Disk 0, and unless i install windows on here (which i cant as its too small) it doesnt boot and find anything because its on disk 1. The laptop is Samsung Series 5 Ultrabook. I will add the model number in a few hours when home.

I dont have any original boot disks im afraid.

Are you trying to install Win 7 on a laptop that came with Win8? If so, did you disabled secure boot on BIOS?
I've seen on a Samsung NP540U3C specs that it has with 24GB ExpressCache.
As the Samsung has installed the OS using some tricks, I would call Samsung and ask for the factory recover disks.

No it's a Windows 7 laptop, and I had reinstalled Windows 7 around 6 months ago and was all ok then, so somehow I must have done something on the first attempt this time that messed the drives around

Model NP530U3C

Have you took a deep look at your BIOS options? For Win 7 secure boot must be disable and CSM set to EFI.
Can it be that the boot loader is being installed on a kind of ramdisk so when you shut it down it vanish?