Try checking the boot order of the drives and make sure the "file only drive" is either last in the boot order or remove it from the boot list if possible.
Also is the drive external/internal?
If its external, make sure the USB option in the boot order is before your SSD. If you installed your OS from a USB stick its quite possible this is the issue.
Another option, the USB or SATA cable might be bad, try swapping it out if you have a spare kicking around.