Problem with 3rd Party SSD's? 2012 Macbook Pro 13

Hello!

I have been having issues with my Macbook Pro, and after searching for a solution for a couple weeks with no results, I am hoping someone can help.

First of all, I am using a mid-2012 13 inch Macbook Pro. It has a 2.5GHZ i5 with 4GB's of RAM.

When I got the laptop, one of the first things I did was install a 256GB Crucial M4 SSD. This set-up worked great for almost 2 years. Then, about 2 weeks ago, everything became incredibly slow. Like all of a sudden. One day everything was fine, and the next the computer was lagging to the point of not being usable. It would power on, and programs would load, but it would take 30+ seconds to respond to a click. And boot times were pitiful.

The first thing I did was wipe my computer, and do a clean reinstall of Yosemite. This didn't help at all.

So I cracked open my computer, and replaced the SSD with the 500GB Hitachi HD that came with the MBP originally. It was running Mountain Lion, But everything worked well. Speeds were back to normal. Or at least what you would expect from a 5400 RPM Hard Drive.

So I thought I had it solved. Something must be wrong with the SSD, right?

So I bought a 120 GB Samsung 850 EVO, installed a fresh copy of Yosemite, and was ready to go. Except, when I put it in my Mac, I was back to the basically unusable lagginess of the original Crucial M4.

And to further verify that the problem was not with the SSD itself, I used the Samsung 850 EVO to boot from an external hard drive enclosure plugged into USB, and didn't have any issues.

So at this point, I am searching for some kind of software issue with 3rd party SSD's installed in the main HD bay. I know it isn't hardware, because it works fine with the original hard, and both of the SSD's work fine when booted from an external enclosure.

Does anyone have any idea what could be causing this?

Thank you for your help!