In my program I have Floating VIs that popup if certain conditions are met. These Floating VIs allow the Main VI to continue running, but remain front most so the user knows there is an issue.
There are also other modal dialogs in the application that could be active when an Floating VI is called in the background. When the Floating VI is called it properly shows up behind the modal dialog and in front of the Main VI.
The problem is that when the modal dialog is dismissed the Floating VI is no longer floating and appears behind the Main VI. Switching focus between VI's will bring either VI to the front. Changing focus to Windows Explorer (clicking on desktop) then back to LabVIEW restores floating behavior to the Floating VI.
I've attached a crude example that exhibits this behavior.
LV 2014 32-bit
WIndows 7 64-bit
I can't offer a solution, but I can verify that the interaction between floating windows and modal dialogs is "hinky" -- though I haven't noticed the effect that you mention.
I've had modal dialogs appear BEHIND the main VI so I couldn't get to them.