The issue of a modal window being left open during debugging, only to jump to the front when the top level vi is run, has been an issue in LabVIEW for as long as I can remember. I am certian that every developer at one time or another experiences this behavior. There are several work arounds to this issue such as "the old 3 fingered salute" (CTRL+ALT+DEL) and kill LabVIEW, programmatically setting the window modality, external VI task managers, etc... however all of them are workarounds to deal with the issue.
The crux of the problem is that any front panel specified as modal immediately becomes modal as soon as the VI is reserved for execution. This proposal would establish additional option to the VI properties dialog (Modal when Executing). Which would only initiate the modal property of the window when the VI was actually executing.
There have been several similar ideas related to dealing with window modality (see below) however I believe this implementation is different than anything I was able to turn up in a search.