SATA cable replaced but not booting 2009 Unibody MacBook Pro but HD boots from USB

Intially I got the greay flashing folder. 
Pulled the drive from the computer and booted it on the same computer with through SATA to USB external reader, no problems.
Ordered a new SATA cable and installed, I have checked all connections for firm snug fitting and proper instalation.
The HD will not boot from inside the computer.
I am in a country that does not have Apple stores and the closest reseller is a great distance away.
Any ideas? 
What could cause this issue?
Thanks!

Try this:
Connect the drive to the MBP as before. Go to Applications / Utilities / Disk Utility. In DU, select the external drive in the left hand column, click First Aid, then Repair Disk. When that is done, do it again. Next click Repair Permissions. After that, quit DU
That process may be all you need to do to get the files you need off the external.

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