Primary hard disk not detected 50% of the times on boot up

I have a Macbook Pro Mid 2012 model with the following changes:

• 16 GB Ram upgrade
• DVD drive replaced with bay and old (existing) 500 GB hard disk for storage
• Main hard drive replaced with 250 GB SSD (Samsung EVO 850)
• Windows 10 via Bootcamp
• Mac OS X Yosemite
• Refind installed on bootup

Recently, my existing SSD hard disk was giving me lots of issues - so I got a new one and SuperDuper'ed the existing one onto it. Formatted the Windows partition and re-installed Windows 10.

I have 50 Gigs on the Mac drive and 200 Gigs on Windows.

The issue that I am facing is that on every other bootup, the Mac does not detect the primary hard disk.

If I press OPTION and hold it, I can see only the 500 Gig data drive (which is not bootable).

I then need to restart and hold COMMAND+R (or D) to get into internet recovery mode, wait till the network selection appears.

Then when I reboot, I am presented with the original hard disk and multiple boot options (Mac / Windows) on Refind.

I don't think it is a refind issue as this occurs even with Refind uninstalled.

This also does not happen when I plug in my old (failing) SSD.

What could be going wrong on the new Hard drive and what can I do to trouble shoot the issue?

Thanks.