Weird SSD problem with 2009 White MacBook

Hi everyone,

I'm running an early 2009 MacBook White (MacBook 5,2 - 2GHz, 4GB) and decided it was time to upgrade from a 500GB HDD to an SSD. I bought a Toshiba 240GB Q300 SSD and an external USB2 enclosure to aid with the transition as well as to put the 500GB HD to work post-upgrade.

My SSD arrived and I connected it to the MacBook using the USB2 interface, and went and clean-installed El Capitan 10.1.1 (I'm wanting a clean break - my home folder has been with me in some form since Panther on my 12" PowerBook) on it. It rebooted from the SSD fine via USB2 and everyone was having a great time. So far so good. I swapped the disks around was all looking forward to having an internal SSD when it just took *ages* to get anywhere. It got to the grey apple logo, the bar appeared and then the progress crawled along until the bar was full and then...nothing. It just sits there, fan going full pelt.

I switched the disks back, and my Yosemite installation on the 500GB HD boots absolutely fine. The SSD booted absolutely fine via USB too. Tried reinstalling El Cap with the SSD in the internal bay and it struggled, installation never completed because on boot-up it just wouldn't boot and got stuck at '19 minutes' remaining.

I returned the SSD and got an exact replacement, assuming there were bad blocks. Just finished installing El Capitan on the new SSD and swapped disks and it arrives at a full progress bar under the apple logo and then just stops, but only when inside the internal bay. I'm running from the SSD as I type this, booted via USB with zero problems. I would assume the SATA interface in the MacBook is bad except for the fact I run into no problems whatsoever with it on the HDD.

TL;DR: My SSD only works via a USB2 connection and won't boot via internal SATA, while my HDD behaves absolutely fine on the same internal connection. What is going on here?