Thanks very much for the kind response and good information. Yes exactly the Balmer lines were not in the right location, I think your response just gave me the insight I needed to move forward. I was mis-using the software as I suspected. Ok so take my data of the reference star and use the on-line resources to create a smoothed instrument result. I was using the on-line resource to create that smoothed result directly. At least that is the first step, and explains the impact. Also getting an idea of the right RMS value is of great help! More to learn for sure, and will always appreciate guidance.
Also thanks for the connection to Woody, he has already contacted me, and I am very happy to have that connection!
Glad to be a beginner part of this group, looking forward to future growth here!