The reported capacity is consistent with a 32-bit LBA limitation. This could be in BIOS or in the SATA driver.
How is the SATA controller configured in BIOS? RAID mode or AHCI mode?
If the motherboard has more than one SATA controller, are the 3TB and 6TB drives attached to the same controller?
Have you updated the SATA controller driver (eg Intel RST) to the latest version?
Does BIOS recognise the full drive capacity?
Note that if your driver has a 32-bit LBA limitation, then your 3TB drive will be a data loss time bomb that will go off when you try to write data beyond the 2TiB point. It would interesting to see how a disc editor such as DMDE (freeware) detects the 3TB drive’s sector range. If it detects an 800GB drive, then this would be of serious concern and would confirm the existence of a 32-bit LBA limitation.