I read about this in the past and there are troubles if the drive is on the other side of a RAID or non-standard SATA. Moving it to the primary SATA 0 seems to fix it.
I could fix the boot disk but not a secondary (D:) disk which is also Samsung EVO 840 series SSD. The Samsung Magician thinks that the secondary disk has the latest firmware (which is EXT0CB6Q), though it is the old one (EXT0BB6Q), thus denying to do anything to it.
Instead of starting the process inside Samsung Magician, first downloading the new firmware, then starting it does not help either because it attacks only the boot disk.
So how can the second disk be fixed?