So I am flying with the Matrice 300 RTK and have limited experience with what I should expect from the data sets after step 1. Assuming I have set up the RTK interface correctly I would expect my data set after step one and after bringing in my ground control to essentially be right on top of each other. The one data set I processed did not and I am certain I was dealing with a fixed position with my base on a point with solid WGS84 and Elipsoid coordinates. What might I be doing wrong?
This sounds like an issue regarding the difference between the ellipsoid versus the geoid heights. The M300RTK will acquire elevations on the WGS84 ellipsoid. However your ground control points might be on a geoid in which case there could be + or - a hundred feet difference between the two. I would suggest verifying what your vertical coordinate system is for your ground control.