Viewing Profile Creates Additional Alignment Line

I created an alignment from lines created in SS3 or SS2 - I copied in the lines, created a civil rule feature for those lines, and then created an alignment using Complex by Elements. Everything seems like it works great. I have my alignment, it's editable, and I can see the report. However - when I go to view the profile it creates a secondary line in the file. What is that line/alignment for? It is not something we want to have, how I can I eliminate it?

Is our workflow wrong with how we create the alignment?

Thanks