I didn’t get much from asking here, but Google’s magical indexing powers brought up a similar thread and while I’m not sure if it is a plugin doing the wrong things, it may be worth a try. Thanks to @mikeowen for that one.
Do you have a machine that doesn’t have any plugins installed on it that we could use as an A/B comparison test? I think if it does render we could install one plugin at a time until it has trouble. The fact that you’re able to run it from the command line leads me to believe that it’s not a GPU issue here. In the past there have been issues with AE not being able to to use GPU acceleration.