I tried your suggestions and get the same behavior. Sometimes the system will boot as it should from the hard drive, other times it will load the OS bootloader (grub) but then fails to boot at what looks like the disk mounting stage. However, most frequently no boot drive is detected by the BIOS at all.
SATA port/cable do not matter. Even tried a second motherboard of the same model, no difference.
This really seems like a BIOS bug to me...