Geoff,
Thanks for continuing to think on my situation.
I've tried what you suggest and I believe this is why it didn't work...
When I pass the path to LabVIEW and use that to get a reference to the VI it is a different reference/instance that TestStand grabs to use when running the Sequence. Ideally whay I would like to do is grab the reference to the VI being used in TestStand pass it to my LabVIEW GUI and use VI Server to manipulate it's size and position to a particular location.
I've found the only way I can make this work is to just manipulate the Sequences VI's ahead of time to lay over the top of my GUI.
Thanks again for all you efforts.