Just as a closing update on this, I first wanted to thank Dan Marsden for all the guidance he has given with helping to troubleshoot this. You've been a great help in finding the source.
End result seems to be that when we turn on completion tracking for a module in the course, it slows down the $cm -> obtain_dynamic_data() call by about 0.1 seconds. This then multiplies by the number of modules we had it on for (about 30) to slow all file loading on the course by 2-3 seconds. This would not be a problem but the SCORM Packages we use load about 30-40 files, so that 2-3 second slow down is multiplied again resulting in 2 minute plus load times.
This does not happen in other courses we have completion tracking enabled and not in our development environment, so it's something specific to our course and production setup. Either way we have a work around for now and the course is running fast again!
Thank you everyone for helping out.