Hello Joseph,
You should be able to do it either way: using VI properties (the method you described) or invoke nodes (the method I described).
I was able to successfully build an application with two VIs (one minimizes at runtime, one stays open) using the VI properties window as you described. When I run the built executable, the VI I configured to minimize at run-time did in fact minimize, and the VI configured to remain opened stayed open. I am not able to replicate the problem on my system (LabVIEW 8.5.1 on Windows XP). Would you mind attaching a simple project which produces the problem?
I've attached the project I created in an attempt to recreate your problem. "minimize.vi" is configured to minimize at run time (no longer has the programmatic minimization method), "normal.vi" is configured to be centered at runtime. Please let me know how the built application behaves on your machine.
Thanks!
Brock
Applications Engineering
National Instruments