This had been bugging me for over a year now. After lots of tinkering, I believe I've found the culprits. Not at all what I expected though. They are:
Expanded Temperature and Pressure Highlight Toolbars

In the video below I demonstrate how just popping up the temperature highlight toolbar suddenly causes the problem. I start the video with me refreshing the plot and running error check before popping up the control bar. Both completed within seconds. Right after I popped up the temperature highlight toolbar, plot refresh took 30 seconds and error check took 6min 45sec to complete.



The same would happen with Pressure Highlight toolbar. And I'm not sure about earlier CAESAR II, but I had the same problem with version 2017.

Again, for smaller models this may not be noticeable. But as I have shown you before, the difference is more obvious the bigger the model becomes. I would love to be able to use these toolbars since I typically deal with multiple temperatures and pressures. Hopefully this problem is taken care of in the next release of CAESAR II.