Thunderbolt Shutting Down when I use CS6

I've read about similar issues when it shuts down, but my case is slightly different.

My Thunderbolt display works fine if I'm browsing the internet or just looking for files, but the moment I boot up any software from my CS6 collection it shuts down. My USB ports also go out randomly, but I'm not sure if it's a different issue or a symptom of what ever is causing this expensive hardware to shut down.

I've installed the firmware update, and I'm running El Capitan 10.11.1.

Do I have to replace an internal board or is this an issue that can be dealt through my keyboard?