Can you please provide below information to analyze more on this issue,
1. mSATA (Disk 1) model and make -
2. Other HDD (Disk 0) model and make -
3. BIOS mode (UEFI/RAID/AHCI) -
Have you injected latest WinPE drivers into boot image?
Have you mentioned any specific disk/drive letter in task sequence to install the OS ?
By default SCCM will choose Disk 0 for OS installation, if the Disk/Drive letter not specifically mentioned in task sequence then it will use default script (diskpartclean.bat) .