I wish I was getting 16 Seconds. My Samsung 840 Pro on a solo x2 is about 20 Seconds boot. The Apple/Samsung is taking 3 times that to boot. Since I'm 300 Mi. Away from my machine right now, it's not annoying me.
At the risk of sounding like the tech support person who asks if your computer is plugged in, did you say you did go into System Preferences and select the Apple/Samsung as the startup drive? I have read in several places that, even though someone took out a drive, the system was looking for it upon startup and only after all else was failing, did it agree to boot from the second choice. Even if this is not the correct answer in your case, I would look around that path. There is no freakin' way that 1 TB Apple blade should take that long to boot, and if everything else is working fine and the read/write speeds are testing okay, I do not believe the problem lies in the drive itself. As you point out, even the 840 PRO boots in 20 seconds, and it is a slower drive.