I am still unable to reproduce your previously discussed issue with more details, but it certainly sounds like the checkbox is not a valid indicator of the true selection and would cause the error you are seeing. An executable will not run if "Remove Panel" is checked on any VI if the front panel should appear when the executable is running.
After building a first executable you may be asked to add some functionnality to it. Several UIs may be added to the project and when configuring the new executable, the "minor display bug" will make this task very unclear. In my case, the "Remove Front Panel" box is not always checked again when displaying the configuration of another VI and then switching back to the previous unchecked one. Sometimes it is, sometimes it is not. How can you then know if a front panel is really removed or not ? I finally opened the .lvproj file to edit it to get a working executable...
Unfortunately, we are aware of the VI Settings bug in LabVIEW 8.20. This was reported to R&D (# 42AA340Z) for further investigation. A possible workaround for this issue is to specify the VI Settings you want in the development environment.
Like mentionned in my previous comment, this is in fact what I do.
Thank you for your time