Hi,
I figured I'd create an account and reply to this as I found this forum whilst trying to solve a similar problem myself.
Through a process of 18% trial and 82% error, I have a working solution to my problem. I thought I would share as it may work with others.
My task sequence begins with a command line which cleans the partitions on disk 0 and disk 1 using diskpart.
I then proceed to partition and format disk 1 (an MSATA disk).
Next comes the installation of Windows (7, 8.1 or 10) on disk 1. I've used this method with all 3.
Apply Windows settings.
Apply Network settings.
ONLY THEN:
Partition and format disk 0.
Apply image to disk 0 (in my case, this is just the program files folders as I need a lot of software in these images).
Finally, set up configuration manager client.
This has worked consistently on around 50 machines with this stupid MSATA set as disk 1 configuration. Sometimes I need to put stuff on disk 0 with the TS, sometimes I don't. Works either way.
By the time you create a partition on disk 0, the computer recognises disk 1 as the boot disk with the OS on it.
Hope this helped at least someone. It gave me a headache for two days...