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In another thread I have explained the issues I have with a clean install of OS X on a SSD.

Now the situation is:

  • Yosemite installed on SSD.
  • Boots from SSD attached via USB .
  • Does not boot from SSD when installed internally.
  • I get a beachball and the Mac will not start.

What might the problem be?

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    The HDD cables of MacBook Pros are known to be very error-prone. You should consider replacing it. iFixit has the knowledge and parts.
    – n1000
    Commented Aug 11, 2015 at 14:39

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Just because the hardware is set to remember where the last boot was from and will look back to it at the bext boot, I can recommend you to hold down the C button right after you start up the fully assembled system and then select the SSD again.

Also note that the cable that connects the internally placed SSD may be damaged/disconnected somehow or even the Motherboard could have a problematic/defected chip.

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