Thank you for helping me out.
I think nothing is wrong with the 2nd SSD because if I remove everything, then insert just two SSDs, both are detected perfectly. If I insert 2x 3.5" and 2x SSD, just the SSDs are detected.
Yes, the SW6 was reset, but the 3.5" drives still don't show up. Detection problem of just the 3.5" HDDs is a mystery to me. How come a backplane (or any other component) differentiates 3.5" SATA from 2.5" SATA? Isn't SATA interface standard for all? Still, if the hot swap cage is replaced, everything seemingly returns back to normal.