This was driving me nuts for almost a week and I finally found the answer, so I decided when I found the answer.
I was running Compressor on a headless Mac Mini server. When I tried to run Compressor on it, the Mini would show the splash screen but then no windows would show. I tried everything, from clearing preferences to a complete re-install of Compressor. Turns out, the issue is the fact that I was running the system as a headless server. If you check the logs, it says that you need an OpenGL compatible display connected. I reconnected a monitor, and that's all it took.
I just wanted to post this in case there's anyone else struggling with this one.