In your LabVIEW project, is the RTEXE build specification configured as 'Set as Startup'? I believe the LabVIEW project will attempt to 'deploy' the project settings each time a VI from the project is interactively run on the target. So if that build spec retains that setting in the project, LabVIEW will overwrite your FALSE .ini token back to TRUE each time you run an interactive FPGA or RT VI in that project.
I haven't been able to verify this behavior, but I suspect if you choose the option 'Unset as startup', that will stop LabVIEW from re-enabling your startup application after you manual set the .ini token to FALSE. In general, this method for setting and unsetting the RTEXE as a startup application is probably more time efficient than manually editing the .ini file, and I've never had issues with the inconsistent behavior you are decribing when using this method.
Regards,
Spex
National Instruments
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