What is the Make & Model of your Sata 3 SSD?
Any Mobo trouble or digital error code lit when it won't boot with the Windows driver installed?
Have you tried to do a Clean Windows install on the Windows SSD?
Try using Windows Troubleshooting Menu (Using Windows Installation or restart PC 3 times in a row) and click on Repair Windows Startup and see if it fixes the Windows SSD Boot Manager Menu.