I have a similar problem and I found my system MBR drive(SSD) was not set as active for some reasons.
Setting system drive as active helps, but after transformation completes and restart, system fails to run few command scripts (just blank cmd appears and disappears without output text).
I believe those scripts should finish merging drives, but it doesn't. Now I have StoreMi drive with partition size of SSD and unlocated partition with size of HDD and system start from SSD, not StoreMi drive. Also on bios start there is no StoreMi logo.
How to fix this?