Writing this while wiping the egg off my face. LOL
I did some testing today. I tried a new seq using the same song and created a map file for the mega tree only. It worked perfect. Went back to my original imported seq and ran just the new mega only map. Now the mega tree was correct. Started on a new song from the same donor and had the same issue with the mega tree not coming right. Deleted all that and started over. Low and behold the map file had the mega tree importing the wrong model. I had a number of them get messed up due to the fact that after you select a model to import, the selection window dropdown closes but the mouse still scrolls the selection. If you are not watching that little window and start scrolling the mouse wheel you will change your mapping. It is necessary to click somewhere outside the model window to effectively close and end that models selection. After I discovered that problem I went back and corrected several of the mappings, but I obviously missed the one for the mega tree. All seems well now, but I wish the selection process would truly close once you do a selection in the drop down box. I'll put a request in github for that.
