Remember to Update Simulationcraft
Remember to keep Simcraft updated! I got better gear and my simulated damage went down. I made sure to use the Simulationcraft addon to import (apparently it can avoid glitches with importing from armory) and updated Simcraft. My simmed damage went up, which was as expected. Thanks to my Shammy buddy who suggested I try updating - it worked. Make sure to keep Simcraft up to date for accurate results.