Here's the easiest fix if that happens:

1) Let it boot into Windows Setup again (ie leave that USB in). Once you get past the welcome screen, hit Shift-F10 
to get a command prompt.

2) Use XCOPY /E /H /R <source> <destination> to copy everything (including hidden files) from that SYSTEM 
partition (on the iSSD) to the partition where you installed Windows. 

Before copying, use DIR /A <driveletter:> commands to determine what the drive letters are for those partitions: 
DIR /A C: and DIR /A D: and DIR /A E: etc. The SYSTEM partition (on the iSSD) should contain a BOOT folder and a 
bootmgr file. The partition where you installed Windows should contain, you guessed it, a Windows folder 

So if your SYSTEM partition (with the boot files) is drive C, and your Windows partition is drive E (for example) use 
the following XCOPY command: XCOPY /E /H /R C:\ E:\ Make sure you get the forward and backward slashes 
right, they're important.

3) Now that the Windows partition contains the necessary boot files, we have to make sure it's flagged Active 
(bootable). Enter the command DISKPART.

4) At the DISKPART> prompt, use LIST DISK to determine the disk number of your HDD (or SDD). Obviously, it's 
the big one (xxx GB) while the small one is the iSSD (xxx MB). Now use SELECT DISK <number> to select the big 
disk, say SELECT DISK 1.

5) Still at the DISKPART> prompt, use LIST PARTITION to determine the partition number of your Windows 
partition. If you installed Windows on a blank disk, it's probably the first partition. Now use SELECT PARTITION 
<number> to select the Windows partition, say SELECT PARTITION 1

6) Still at the DISKPART> prompt, use DETAIL PARTITION to verify you got the right partition.

7) Still at the DISKPART> prompt, use ACTIVE to flag your (now selected) Windows partition Active and bootable.

8) Use Exit to leave DISKPART. Exit again to leave the command prompt. Close down Windows setup. Remove the 
USB. Reboot.

(Sorry for the detail, I didn't know if you're familiar with DOS/Windows command syntax. And even if you are, it 
may help others).

I've done this several times, works like a charm and only takes a few mins extra. You won't have a separate 
SYSTEM partition -- which I prefer not to have anyway. But if you use BitLocker (Win7 Ultimate) I think it needs 
that.

Let me know how it goes.

Update: I see comments from yourself and others indicating this might be a hardware or IRQ problem. I apologize if 
I missed an earlier context and your problem is a different one.

It is a very common problem when installing Windows from USB onto Series 5 and Series 7 that Windows Setup 
mistakenly assumes the iSSD (ExpressCache) to be the boot drive, which causes it to fail booting. The above steps 
are (in my opinion) the simplest solution to this -- although there are others.

Windows Setup mistakenly assumes the iSSD (ExpressCache) to be the boot drive, which causes it to fail booting.