Hi Sean,
Thanks for the details. I have spoken with the Simbrief team, and it is very unlikely that this has anything to do with the profile itself, buuut… It looks a little strange that these missing waypoints are in the TOC/TOD. Therefore, we have involved another team to analyze this as well.
I still can’t promise anything, as no one on our team can reproduce it, but I want to let you know we are still working to identify the issue. It’s essential not only for you, but also for us 
Thanks again for your patience and your help in this case
Richard