I also see this from time-to-time. But its not consistent, and I have not been diligent enough to figure out a pattern.
With all of Windows security features, you might find it difficult to add something to your plug-in to always bring Rhino to the front. But most likely it will involve p/invoke and some Win32 function, such as SetWindowPos().
Thought of something like that. I need this because else my “Manager” stays on top and I’m afraid people will close it to get to Rhino. And my plugin gets a lot of information out of my “Manager”.