would you try a clipped viewport with the viewport layer off please? That seems to be the condition that is required for me to replicate the problem. I would like to see if you can produce the same result.
Clipped is a problem apparently. Most of my viewports are clipped, but I tested last time in the default 'Layout 1' because I didn't have any set up. This time I had two viewports, one clipped, one standard, and used Ctrl+R to toggle back & forth. Standard viewport shows a border the same colour as paperspace crosshairs, clipped viewport shows no border at all.
So I can't replicate what you're seeing, but there is an issue here.
Again, I'm in 2011, so I'm sure something's changed since.
Credit where credit is due! Give kudos or accept as solution whenever you can.
I have noticed one thing about overlapping viewports and this may be your trouble. The bigger view port is almost allways the one gets selected. Have you tried to see if your active viewport is actually the smaller one. To get the viewports to react as would be expected, I have started to clip all of them so there is very little overlap. That has fixed my issues. It takes a little longer, but I do a Clip and select polygon.
In the case of my IP (and most of my layouts with the majority of this problem) there is only the one viewport.