I tried launching it through the terminal with the command you gave me, but it didn't do anything differently. I don't think it is with KSP itself, but rather something about my computer and the way it runs KSP. The whole OS is running at a very slow frame-rate, but the CPU is around 15%-20%. It isn't the ram either, that less than half used.
Thanks for trying. By the way, where did you learn about the command-line graphics options? Just curious.