kph,
If you run the sequence, do you see any problems related to passing the data between TestStand and the VI? I am assuming that the prototype you see is exactly the same when TestStand asks you to reload the prototype. It is possible that TestStand may be finding different versions of the VI on you system due to your search directories. If you have multiple copies of the VI, TestStand may find different version of the VI than you think it is loading. This is especially true if you have a network drive that may be changing. You may want to create a test VI with an absolute path to test this theory.
Which versions of TestStand and LabVIEW are you using?
Let me know if you find any more information.
Thanks,
Tyler