I would have to assume an image would include everything it needed to get your system back to its original state. So putting some of the required folders on a second drive might be your problem. I do not know exactly what those things are but perhaps testing without the HDD installed would let you know when the image you want can be created.
The system will boot to the first active partition it finds. If you system boots to the SSD with the HDD disconnected, you might want to make sure the HDD does not have an active partition if you, for some reason, cannot change the order of the drives in the bios. Disk Management will show which partitions are active. And unless you are running an UEFI bios system, the partition with the boot files has to be active.