SSD upgrade running terrible in main bay but fine in external case enclosure

Question

Hi,
I'm having major issues trying to upgrade my Macbook Pro (13" mid-2012.  OS X 10.9.5) HD from standard apple installed Toshiba 750GB (which ran Maveriks) to a Samsung EVO 1TB SSD.  First I installed the SSD into the HD main bay, formatted as per apple support instructions (mac extended journaled) and installed Yosemite from a bootable USB, transferred documents from my time machine and reinstalled a variety of applications.  Seemed to work OK for a while but then many strange error messages began appearing.  The main one was "unapproved caller error- security agent may only be invoked by apple software.  I also had trouble coping files from my time machine (error message said the files couldn't be read or written), but when tested on another mac worked fine.  Safari kept freezing and when I tried to download apps said there was not enough disk space - there was plenty! When trying to open the apple store app the icon appeared in the dock briefly and then closed again. Over the preceding hour more and more of these errors appeared and eventually the computer was unusable, the screen went black with only the unauthorised caller error.  I decided to start again and this time install OS X from internet recovery.  Reformatted the drive as usual and booted with CMD + R.  First internet recovery didn't work- error apple couldn't create a recovery partition.  I used disk utility to verify the disk, Got - "the partition map needs to be repaired because there is a problem with the EFI system partitions file system".  Used "repair disk" to resolve this.  Tried the install again, failed again, can't remember the error message but it was different then the first.
After searching the internet and not finding anything helpful I decided to try cloning my old HD onto the new SSD using carbon copier with SSD in external caddy.  Now works totally fine in the external caddy but as soon as I put it in the internal bay it again is very slow, gives funny errors such as "This operation can not be completed because an unexpected error occurred (error code 50)".  Also keeps freezing, wont let me delete any apps/files and generally after about 10 mins becomes unusable and I have to restart.  It boots fine to start with though. 
I previously had problems with the old HD freezing and being very very slow.  Apple replaced it about 8 months ago and it seems OK but is much slower then I would expect from an i7.   The only thing I have seen on forums is possible the SATA cable may be the problem???
Anybody have a clue what is going on!?!??! Please help!  I would take it into the apple store as its still under warranty but I'm assuming they wont support it as its not one of their HDs and also I installed it myself.  Also macbook is still working fine with old HD.
Help!

Answer 1

>I decided to try cloning my old HD onto the new SSD....works totally fine in the external caddy but as soon as I put it in the internal bay it again is very slow, gives funny errors.......I previously had problems with the old HD freezing and being very very slow. ..... possible the SATA cable may be the problem???<
Almost certainly and what you did pretty much proves it. So you'd have to examine the SATA cable and connection to the logic board for damage. Then try replacing it. It's not exactly cheap so make sure before you buy:
https://www.ifixit.com/Guide/MacBook+Pro+13-Inch+Unibody+Mid+2012+Hard+Drive+Cab le+Replacement/10379
Wonder if the hardware test would find this problem.
Then there's this:
http://www.macworld.com/article/2030013/advice-from-an-apple-tech-three-common-m ac-fixes.html
"The 13-inch MacBook Pro notebook from mid-2011 is an outstanding computer, but some of these laptops apparently were made with a bad batch of hard drive cables that failed after about a year."
and:
http://apple.stackexchange.com/questions/73956/macbook-pro-hard-drive-problems-c an-it-be-hard-drive-cable