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Loading VI Dialog from EXE

I have a project which I duplicated the .lvproj file and all dependencies from LabVIEW. I confirmed that all the files are being loaded from the proper locations via the files view and making sure there are no conflicts in the project. The issue is that after I build an executable and launch it, I get the LabVIEW dialog popup which loads a number of VIs from the EXE.

EXE VI Loading.png

Then the EXE starts and runs normally but then when I exit the EXE I get a prompt to save various VIs:

After EXE Close.png

I have opened each of these VIs and their callers to make sure everything loads correctly in the dev environment and I have also done a mass compile on both my project directory and even user.lib and vi.lib but to no avail. I have also tried creating a new build spec. Any suggestions?

Carlton
CLA
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As a follow-up, the same issue happens if I add my main VI to a new project with a new build spec.

Carlton
CLA
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If LabVIEW can not find VIs in exe, it means they have not been included. If it finally loads VIs from original source code, it is not good.

Most often it happens because they are called dynamically by reference, then they must be included manually into exe. 

Also check the Additional Exclusions section if anything applies to these VIs and try to reduce exclusion. 

Also check old project settings (tabs: Additional exclusions, Source Files: Always included files, Source file settings) and structure (you can not configure build settings for items from dependencies!).

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