So whats the question??
Do you want to know why the SATA 2 hdd is slow on the SATA 3 port? Or why the PCI-E SATA 3 card is slow?
If you plug a SATA 2 hdd into either it wont be as fast as SATA3. You'll have to buy a SATA 3 hdd
SATA 3 supports SATA 2, but it wont change SATA 2 speed to SATA 3 speed