Issues putting a hard drive in the optical bay of my early 2011 MacBook Pro
Firstly, it does not seem to really matter whether you use the Sata II or III port. For most usages you won't see the difference, cf this post for details: http://www.tomshardware.com/forum/280002-32-sata-sata-practical-difference.

Given that the disk shows up fine via a USB interface it means that it's not at fault so it could actually be due to the connector in the optical bay which is a bit worn out or that the drive is not correctly plugged.

Try putting the HD in the original HD bay and the SSD in the optical bay and see if the SSD has the same issue. If it has then the issue lies with the optical bay itself.

You could also put the optical disk back into the bay and see if it works normally or has issues as well.

If the issue seems to stem from the optical bay then you should bring the computer to a shop which can diagnose exactly what hardware issue is causing this.