I found my problem. In short, I increased my Computer Sleep and Display Sleep time in the Energy Saver of the System Preferences to 2 hours. They were set to 15 mins and my plots were taking much longer. I happen to notice that the plot stopped when my screen saver turned on. Although, it was not my screen saver but my Computer Sleep. Since the change, I have plotted a few things that took some time. The last plot was an svg that contained 5000 points and it took 45 mins to complete.
I feel confident that this was my problem. Thanks for all the responses. This might be worth putting in the wiki. That is, make sure your computer is not set to sleep during your plot.