Several issues only with executable, not in VI

Hello, I'm developing a program to control a network analyzer from GPIB, store data, read that data into some matlab (math script) routines to determine pass/fail and plot a pattern, then save a screen-grab of that pass/fail/pattern. Everything works as I expect it to in the development environment, but when I build it into an executable and run it on the same development machine, weird things start to happen that I don't understand. I know from past that executables run faster than vi's so I have added time delays here and there where it seems to make sense for that particular bit of code, but even that has not helped.
There are 3 main issues:
1.) I populate a listbox from a folder with filenames that match a pattern. This works great. There is an event structure that waits for one of the files to be selected which then sends that file into a subvi that runs through the mathscript routines. Problem is in the executable, after this mathscript subvi executes, all the contents of the listbox disapear and I can't select another file to run through the mathscript code. stopping and starting the main app re-reads this in but it should be read in continuously because its in the main programs for-loop.
2.) The mathscript routines were developed by someone else, they are in several nodes. The first two nodes work perfectly to generate 2 patterns, find beam peak, position, and beamwidth, but the next two, which are identical, don't seem to work in the executable. They should produce sidelobe levels, but don't.
3.) The screen-grab bit doesn't work in the executable either, I found a vi from Alex T. (https://decibel.ni.com/content/docs/DOC-19720) that automates a print screen event and then reads the clipboard to output image data which I then save as a jpg or png. This I had to add delays in to get the vi to work, but it still doesn't work in the executable.
Any help or ideas would be greatly appreciated. Even if its just the basics- I'm pretty much self-taught  and don't profess to know the best way or even the right way
Jamie
Attachments:
Phase Scanner_S Folder.zip ‏4123 KB
main code.jpg ‏753 KB
mathscript subvi.jpg ‏753 KB

Error code -90093:  LabVIEW:  The LabVIEW Run-Time Engine does not support this function.
Looks like you are using something that is not available in the RTE.
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