Solution
This behavior is expected to happen when the Execution Profiler has not had enough time to finish processing event updates from the running sequence. Since the .NET calls to the Execution Profiler from within TestStand are happening quickly, it doesn't get a final update from all pending events at the moment of saving the .tpf file.
To ensure that all previous steps and events have finished reporting their updates to the Execution Profiler, include the ProcessPendingEvents method before calling the Save method. You can also exclude the Execution Profiler steps from the profile itself by following the steps in this link, Excluding Items from Profiling - NI .
Below is an image of the updated Exit_Execution_Profiler sequence shown above but with the added ProcessPendingEvents method:
